diff --git a/.github/workflows/update-gpu-snapshot.yml b/.github/workflows/update-gpu-snapshot.yml index ac27b8167..40314d173 100644 --- a/.github/workflows/update-gpu-snapshot.yml +++ b/.github/workflows/update-gpu-snapshot.yml @@ -7,10 +7,10 @@ on: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver - NFT_VER: "0.9.2" + NFT_VER: "0.9.3" NXF_ANSI_LOG: false # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver - NXF_VER: "24.10.5" + NXF_VER: "25.04.0" jobs: update-gpu-snapshot: diff --git a/.nf-core.yml b/.nf-core.yml index ca13cb160..38640f716 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -6,6 +6,7 @@ lint: files_unchanged: - docs/images/nf-core-methylseq_logo_light.png - docs/images/nf-core-methylseq_logo_dark.png + - assets/nf-core-methylseq_logo_light.png modules_config: false nf_core_version: 3.5.1 repository_type: pipeline diff --git a/CHANGELOG.md b/CHANGELOG.md index f43604511..bcb81c352 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Bug fixes & refactoring - 🐛 Fix error in `picard_bedtointervallist.config` [#566](https://github.com/nf-core/methylseq/pull/566) +- 🐛 Fix error when using --aligner bwameth with samtools sort, the output bams will be labeled with prefix "${meta.id}.deduplicated.sorted" and published in the deduplication folder [#580](https://github.com/nf-core/methylseq/pull/581) - 🔧 Update Bismark to v0.25.1 [#569](https://github.com/nf-core/methylseq/pull/569) - 🔧 Update MultiQC module diff --git a/README.md b/README.md index 58e2261b2..196c52ba6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@

- - nf-core/methylseq + + nf-core/methylseq

diff --git a/assets/nf-core-methylseq_logo_light.png b/assets/nf-core-methylseq_logo_light.png index 8be28a927..e356692e4 100644 Binary files a/assets/nf-core-methylseq_logo_light.png and b/assets/nf-core-methylseq_logo_light.png differ diff --git a/conf/modules/bwamem_align.config b/conf/modules/bwamem_align.config new file mode 100644 index 000000000..fba69f109 --- /dev/null +++ b/conf/modules/bwamem_align.config @@ -0,0 +1,11 @@ +process { + withName: BWA_MEM { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/${params.aligner}/alignments" }, + pattern: "*.bam", + mode: params.publish_dir_mode, + enabled: params.save_align_intermeds + ] + } +} diff --git a/conf/modules/bwameth_align.config b/conf/modules/bwameth_align.config index bc4ab7580..d660b174a 100644 --- a/conf/modules/bwameth_align.config +++ b/conf/modules/bwameth_align.config @@ -1,6 +1,5 @@ process { withName: BWAMETH_ALIGN { - cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain ext.args = '' publishDir = [ path: { "${params.outdir}/${params.aligner}/alignments" }, diff --git a/conf/modules/samtools_sort.config b/conf/modules/samtools_sort.config index 95c78bd0c..83de73995 100644 --- a/conf/modules/samtools_sort.config +++ b/conf/modules/samtools_sort.config @@ -1,29 +1,12 @@ process { withName: SAMTOOLS_SORT { - ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" } + ext.prefix = { "${meta.id}.sorted" } publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.deduplicated.sorted.bam" - ], [ path: { "${params.outdir}/${params.aligner}/alignments/" }, mode: params.publish_dir_mode, pattern: "*.sorted.bam", - enabled: params.skip_deduplication - ], - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*markdup*.bam", - enabled: params.save_align_intermeds - ], - [ - path: { "${params.outdir}/${params.aligner}/alignments/" }, - mode: params.publish_dir_mode, - pattern: "*.bam", - enabled: params.save_align_intermeds + enabled: params.skip_deduplication || params.save_align_intermeds ] ] } diff --git a/conf/subworkflows/fastq_align_dedup_bismark.config b/conf/subworkflows/fastq_align_dedup_bismark.config index 7531de5a9..ac190f50f 100644 --- a/conf/subworkflows/fastq_align_dedup_bismark.config +++ b/conf/subworkflows/fastq_align_dedup_bismark.config @@ -6,3 +6,25 @@ includeConfig "../modules/bismark_methylationextractor.config" includeConfig "../modules/bismark_coverage2cytosine.config" includeConfig "../modules/bismark_report.config" includeConfig "../modules/bismark_summary.config" + +// Override SAMTOOLS_SORT for bismark workflow +// In bismark, deduplication (BISMARK_DEDUPLICATE) happens BEFORE sorting, +// so the BAM input to SAMTOOLS_SORT is already deduplicated when skip_deduplication is false +process { + withName: SAMTOOLS_SORT { + ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.deduplicated.sorted.bam" + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.sorted.bam", + enabled: params.skip_deduplication + ] + ] + } +} diff --git a/conf/subworkflows/fastq_align_dedup_bwamem.config b/conf/subworkflows/fastq_align_dedup_bwamem.config index f0e97bad0..e0a698b7c 100644 --- a/conf/subworkflows/fastq_align_dedup_bwamem.config +++ b/conf/subworkflows/fastq_align_dedup_bwamem.config @@ -1,2 +1,4 @@ +includeConfig "../modules/bwamem_align.config" includeConfig "../modules/picard_addorreplacereadgroups.config" -includeConfig "../modules/picard_removeduplicates.config" +includeConfig "../modules/picard_markduplicates.config" +includeConfig "../modules/samtools_index.config" diff --git a/modules.json b/modules.json index 4cf121414..e3a46b328 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "bismark/align": { "branch": "master", - "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", "installed_by": ["fastq_align_dedup_bismark"] }, "bismark/coverage2cytosine": { @@ -28,7 +28,7 @@ "bismark/genomepreparation": { "branch": "master", "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c", - "installed_by": ["fasta_index_bismark_bwameth"] + "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] }, "bismark/methylationextractor": { "branch": "master", @@ -48,12 +48,12 @@ "bwa/index": { "branch": "master", "git_sha": "1c46359c837ef768b004519f535c30378e8289fc", - "installed_by": ["modules"] + "installed_by": ["fasta_index_methylseq"] }, "bwa/mem": { "branch": "master", "git_sha": "1c46359c837ef768b004519f535c30378e8289fc", - "installed_by": ["modules"] + "installed_by": ["fastq_align_bwa"] }, "bwameth/align": { "branch": "master", @@ -63,7 +63,7 @@ "bwameth/index": { "branch": "master", "git_sha": "79f1c3e487520405be6dd47ed7f196efd1e3b63e", - "installed_by": ["fasta_index_bismark_bwameth"] + "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] }, "cat/fastq": { "branch": "master", @@ -72,27 +72,27 @@ }, "fastqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["fasta_index_bismark_bwameth"] + "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] }, "methyldackel/extract": { "branch": "master", "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0", - "installed_by": ["fastq_align_dedup_bwameth", "modules"] + "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"] }, "methyldackel/mbias": { "branch": "master", "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0", - "installed_by": ["fastq_align_dedup_bwameth", "modules"] + "installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"] }, "multiqc": { "branch": "master", - "git_sha": "8deffd6a402233ebf905c66dbf804bd4c2637946", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", "installed_by": ["modules"] }, "parabricks/fq2bammeth": { @@ -103,7 +103,7 @@ "picard/addorreplacereadgroups": { "branch": "master", "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bwamem"] }, "picard/bedtointervallist": { "branch": "master", @@ -123,7 +123,7 @@ "picard/markduplicates": { "branch": "master", "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255", - "installed_by": ["fastq_align_dedup_bwameth"] + "installed_by": ["fastq_align_dedup_bwamem", "fastq_align_dedup_bwameth"] }, "preseq/lcextrap": { "branch": "master", @@ -143,52 +143,61 @@ "rastair/call": { "branch": "master", "git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8", - "installed_by": ["modules"] + "installed_by": ["bam_taps_conversion"] }, "rastair/mbias": { "branch": "master", "git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8", - "installed_by": ["modules"] + "installed_by": ["bam_taps_conversion"] }, "rastair/mbiasparser": { "branch": "master", "git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9", - "installed_by": ["modules"] + "installed_by": ["bam_taps_conversion"] }, "rastair/methylkit": { "branch": "master", "git_sha": "0dca361fb441760fb333467b3f5800d34490fb86", - "installed_by": ["modules"] + "installed_by": ["bam_taps_conversion"] }, "samtools/faidx": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["fasta_index_bismark_bwameth"] + "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] }, "samtools/flagstat": { "branch": "master", "git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45", - "installed_by": ["fastq_align_dedup_bwameth"] + "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"] }, "samtools/idxstats": { "branch": "master", "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", - "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth"] + "installed_by": [ + "bam_sort_stats_samtools", + "fastq_align_dedup_bismark", + "fastq_align_dedup_bwamem", + "fastq_align_dedup_bwameth" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth"] + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", + "installed_by": [ + "bam_sort_stats_samtools", + "fastq_align_dedup_bismark", + "fastq_align_dedup_bwameth" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", - "installed_by": ["fastq_align_dedup_bwameth"] + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", + "installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"] }, "trimgalore": { "branch": "master", @@ -198,25 +207,60 @@ "untar": { "branch": "master", "git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408", - "installed_by": ["fasta_index_bismark_bwameth"] + "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"] } } }, "subworkflows": { "nf-core": { + "bam_methyldackel": { + "branch": "master", + "git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0", + "installed_by": ["subworkflows"] + }, + "bam_sort_stats_samtools": { + "branch": "master", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", + "installed_by": ["fastq_align_bwa"] + }, + "bam_stats_samtools": { + "branch": "master", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", + "installed_by": ["bam_sort_stats_samtools"] + }, + "bam_taps_conversion": { + "branch": "master", + "git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9", + "installed_by": ["subworkflows"] + }, "fasta_index_bismark_bwameth": { "branch": "master", "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c", "installed_by": ["subworkflows"] }, + "fasta_index_methylseq": { + "branch": "master", + "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428", + "installed_by": ["subworkflows"] + }, + "fastq_align_bwa": { + "branch": "master", + "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4", + "installed_by": ["fastq_align_dedup_bwamem"] + }, "fastq_align_dedup_bismark": { "branch": "master", - "git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c", + "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428", + "installed_by": ["subworkflows"] + }, + "fastq_align_dedup_bwamem": { + "branch": "master", + "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428", "installed_by": ["subworkflows"] }, "fastq_align_dedup_bwameth": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { @@ -226,7 +270,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", + "git_sha": "df4d1c8cdee98a1bbbed8fc51e82296568e0f9c1", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index b367a0719..dfc4707fb 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -16,7 +16,7 @@ process BISMARK_ALIGN { tuple val(meta), path("*bam") , emit: bam tuple val(meta), path("*report.txt"), emit: report tuple val(meta), path("*fq.gz") , emit: unmapped, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("bismark"), eval('bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs'), topic: versions, emit: versions_bismark when: task.ext.when == null || task.ext.when @@ -61,11 +61,6 @@ process BISMARK_ALIGN { --genome ${index} \\ --bam \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') - END_VERSIONS """ stub: @@ -74,10 +69,5 @@ process BISMARK_ALIGN { """ touch ${prefix}.bam touch ${prefix}.report.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml index cc87a6d2d..b88fa4b07 100644 --- a/modules/nf-core/bismark/align/meta.yml +++ b/modules/nf-core/bismark/align/meta.yml @@ -85,13 +85,27 @@ output: description: Output FastQ file(s) containing unmapped reads pattern: "*.{fq.gz}" ontologies: [] + versions_bismark: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bismark: + type: string + description: The tool name + - 'bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs': + type: string + description: The version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - bismark: + type: string + description: The tool name + - 'bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs': + type: string + description: The version of the tool authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test index 2148b91a1..b2fe71b6f 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -53,8 +53,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), process.out.unmapped, - process.out.versions, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) @@ -92,8 +91,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), process.out.unmapped, - process.out.versions, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) @@ -128,8 +126,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), process.out.unmapped, - process.out.versions, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) @@ -167,8 +164,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), process.out.unmapped, - process.out.versions, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) @@ -203,8 +199,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"), process.out.unmapped, - process.out.versions, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) diff --git a/modules/nf-core/bismark/align/tests/main.nf.test.snap b/modules/nf-core/bismark/align/tests/main.nf.test.snap index a2231d4da..70915fb3c 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/align/tests/main.nf.test.snap @@ -5,21 +5,22 @@ true, [ - ], - [ - "versions.yml:md5,72777174718c419301be78c0840f1931" ], { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - } + "versions_bismark": [ + [ + "BISMARK_ALIGN", + "bismark", + "0.25.1" + ] + ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.10.0" }, - "timestamp": "2025-09-26T12:09:08.59445088" + "timestamp": "2025-10-28T15:31:46.994204006" }, "hisat2 | paired-end | sarscov2 genome [fasta]": { "content": [ @@ -27,21 +28,22 @@ false, [ - ], - [ - "versions.yml:md5,72777174718c419301be78c0840f1931" ], { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - } + "versions_bismark": [ + [ + "BISMARK_ALIGN", + "bismark", + "0.25.1" + ] + ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.10.0" }, - "timestamp": "2025-09-26T12:08:47.207193467" + "timestamp": "2025-10-28T15:31:21.888003798" }, "bowtie2 | paired-end | sarscov2 genome [fasta]": { "content": [ @@ -49,21 +51,22 @@ false, [ - ], - [ - "versions.yml:md5,72777174718c419301be78c0840f1931" ], { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - } + "versions_bismark": [ + [ + "BISMARK_ALIGN", + "bismark", + "0.25.1" + ] + ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.10.0" }, - "timestamp": "2025-09-26T12:08:02.040747075" + "timestamp": "2025-10-28T15:30:37.313541027" }, "bowtie2 | single-end | sarscov2 genome [fasta]": { "content": [ @@ -71,21 +74,22 @@ true, [ - ], - [ - "versions.yml:md5,72777174718c419301be78c0840f1931" ], { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - } + "versions_bismark": [ + [ + "BISMARK_ALIGN", + "bismark", + "0.25.1" + ] + ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.10.0" }, - "timestamp": "2025-09-26T12:07:37.985126432" + "timestamp": "2025-10-28T15:30:15.340678938" }, "hisat2 | single-end | sarscov2 genome [fasta]": { "content": [ @@ -93,20 +97,21 @@ true, [ - ], - [ - "versions.yml:md5,72777174718c419301be78c0840f1931" ], { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - } + "versions_bismark": [ + [ + "BISMARK_ALIGN", + "bismark", + "0.25.1" + ] + ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.10.0" }, - "timestamp": "2025-09-26T12:08:24.007957857" + "timestamp": "2025-10-28T15:30:58.182901875" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 23e16634c..4b3041dc5 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -11,9 +11,9 @@ process FASTQC { tuple val(meta), path(reads) output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions + tuple val(meta) , path("*.html") , emit: html + tuple val(meta) , path("*.zip") , emit: zip + tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions when: task.ext.when == null || task.ext.when @@ -43,11 +43,6 @@ process FASTQC { --threads ${task.cpus} \\ --memory ${fastqc_memory} \\ ${renamed_files} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ stub: @@ -55,10 +50,5 @@ process FASTQC { """ touch ${prefix}.html touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index c8d9d025a..f988697a2 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -53,13 +53,27 @@ output: description: FastQC report archive pattern: "*_{fastqc.zip}" ontologies: [] + versions_fastqc: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//: + type: string + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//: + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a074..66c44da9b 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -58,7 +58,7 @@ nextflow_process { { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -82,7 +82,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -106,7 +106,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -142,7 +142,7 @@ nextflow_process { { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db3092f..c8ee120f5 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,15 +1,21 @@ { "sarscov2 custom_prefix": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2025-10-28T16:39:14.518503" }, "sarscov2 single-end [fastq] - stub": { "content": [ @@ -33,7 +39,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -44,8 +54,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -59,10 +73,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:24.993809" + "timestamp": "2025-10-28T16:39:19.309008" }, "sarscov2 custom_prefix - stub": { "content": [ @@ -86,7 +100,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -97,8 +115,12 @@ "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -112,58 +134,82 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:03:10.93942" + "timestamp": "2025-10-28T16:39:44.94888" }, "sarscov2 interleaved [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:42.355718" + "timestamp": "2025-10-28T16:38:45.168496" }, "sarscov2 paired-end [bam]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:53.276274" + "timestamp": "2025-10-28T16:38:53.268919" }, "sarscov2 multiple [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:05.527626" + "timestamp": "2025-10-28T16:39:05.050305" }, "sarscov2 paired-end [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:31.188871" + "timestamp": "2025-10-28T16:38:37.2373" }, "sarscov2 paired-end [fastq] - stub": { "content": [ @@ -187,7 +233,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -198,8 +248,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -213,10 +267,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:34.273566" + "timestamp": "2025-10-28T16:39:24.450398" }, "sarscov2 multiple [fastq] - stub": { "content": [ @@ -240,7 +294,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -251,8 +309,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -266,22 +328,28 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:03:02.304411" + "timestamp": "2025-10-28T16:39:39.758762" }, "sarscov2 single-end [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:19.095607" + "timestamp": "2025-10-28T16:38:29.555068" }, "sarscov2 interleaved [fastq] - stub": { "content": [ @@ -305,7 +373,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -316,8 +388,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -331,10 +407,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:44.640184" + "timestamp": "2025-10-28T16:39:29.193136" }, "sarscov2 paired-end [bam] - stub": { "content": [ @@ -358,7 +434,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -369,8 +449,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -384,9 +468,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:53.550742" + "timestamp": "2025-10-28T16:39:34.144919" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index abbef4566..335afccc4 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -18,7 +18,7 @@ process MULTIQC { path "*.html" , emit: report path "*_data" , emit: data path "*_plots" , optional:true, emit: plots - path "versions.yml", emit: versions + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), topic: versions, emit: versions_multiqc when: task.ext.when == null || task.ext.when @@ -42,11 +42,6 @@ process MULTIQC { ${replace} \\ ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: @@ -56,9 +51,5 @@ process MULTIQC { mkdir multiqc_plots touch multiqc_report.html - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 9ac86fd11..4a9086116 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -28,8 +28,8 @@ input: - edam: http://edamontology.org/format_3750 # YAML - extra_multiqc_config: type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. + description: Second optional config yml for MultiQC. Will override common + sections in multiqc_config. pattern: "*.{yml,yaml}" ontologies: - edam: http://edamontology.org/format_3750 # YAML @@ -73,13 +73,27 @@ output: description: Plots created by MultiQC pattern: "*_data" ontologies: [] + versions_multiqc: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g: + type: string + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g: + type: string + description: The command used to generate the version of the tool authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 0745e25ab..d1ae8b06c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() } ) } @@ -82,7 +82,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() } ) } } @@ -110,7 +110,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index a88bafd67..f76049d3b 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,61 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "versions_multiqc": [ + [ + "MULTIQC", + "multiqc", + "1.32" + ] + ] + } ], "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-27T13:33:24.356715" + "timestamp": "2025-10-28T15:27:59.813370216" }, - "multiqc_stub": { + "sarscov2 single-end [fastqc] - stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" + { + "versions_multiqc": [ + [ + "MULTIQC", + "multiqc", + "1.32" + ] + ] + } ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-27T13:34:11.103619" + "timestamp": "2025-10-28T15:30:48.963962021" }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] [config]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "versions_multiqc": [ + [ + "MULTIQC", + "multiqc", + "1.32" + ] + ] + } ], "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-10-27T13:34:04.615233" + "timestamp": "2025-10-28T15:29:30.664969334" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index d4bd5a327..6b5aa31dd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -19,7 +19,7 @@ process SAMTOOLS_SORT { tuple val(meta), path("${prefix}.${extension}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true tuple val(meta), path("${prefix}.${extension}.bai"), emit: bai, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -53,10 +53,6 @@ process SAMTOOLS_SORT { -o ${output_file} \\ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -78,9 +74,5 @@ process SAMTOOLS_SORT { touch ${prefix}.${extension} ${index} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 4c4010bbb..809a57fcf 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -76,7 +76,6 @@ output: description: Sorted SAM file pattern: "*.{sam}" ontologies: [] - crai: - - meta: type: map @@ -110,13 +109,28 @@ output: description: BAM index file (optional) pattern: "*.bai" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index ff0691906..df47bb25c 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -34,7 +34,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -66,7 +66,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -98,7 +98,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -133,7 +133,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -168,7 +168,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -203,7 +203,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -235,7 +235,7 @@ nextflow_process { { assert snapshot( process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -265,7 +265,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } @@ -296,7 +296,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } @@ -325,7 +325,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 473e17450..4e618fa3f 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -19,80 +19,21 @@ "test.sorted.cram.crai" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T14:43:31.395604" - }, - "bam - stub": { - "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:37.387063" + "timestamp": "2025-10-29T12:47:01.171084" }, "bam_csi_index": { "content": [ @@ -114,15 +55,39 @@ "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:06.976036" + "timestamp": "2025-10-29T12:46:00.961675" + }, + "bam - stub": { + "content": [ + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-10-29T12:47:12.154354" }, "multiple bam bai index": { "content": [ @@ -144,80 +109,39 @@ "test.sorted.bam.bai" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:18.72271" + "timestamp": "2025-10-29T12:46:25.488622" }, "cram - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ - - ], - "crai": [ - - ], - "cram": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:48.734367" + "timestamp": "2025-10-29T12:47:28.485045" }, "multiple bam": { "content": [ @@ -233,80 +157,39 @@ [ ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:12.989244" + "timestamp": "2025-10-29T12:46:13.168476" }, "multiple bam - stub": { "content": [ { - "0": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" - ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:43.196638" + "timestamp": "2025-10-29T12:47:21.628088" }, "bam_no_index": { "content": [ @@ -322,15 +205,21 @@ [ ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:42:54.926504" + "timestamp": "2025-10-29T12:45:47.139418" }, "multiple bam csi index": { "content": [ @@ -352,45 +241,21 @@ "test.sorted.bam.csi" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T14:43:25.059178" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi" + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] ] - ], - [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" - ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-10-08T11:59:46.372244" + "timestamp": "2025-10-29T12:46:51.5531" }, "bam_bai_index": { "content": [ @@ -412,14 +277,20 @@ "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:00.82974" + "timestamp": "2025-10-29T12:45:52.796936" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index c06ad3bf6..cc8ee59fe 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -13,7 +13,7 @@ process SAMTOOLS_STATS { output: tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -28,21 +28,11 @@ process SAMTOOLS_STATS { ${reference} \\ ${input} \\ > ${prefix}.stats - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.stats - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 6dc51885d..a20509ae6 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -55,13 +55,28 @@ output: description: File containing samtools stats output pattern: "*.{stats}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //: + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - samtools version | sed "1!d;s/.* //: + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index a451c04e6..94d981b2a 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -23,16 +27,20 @@ "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba" ] ], - "versions": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T15:05:52.878044" + "timestamp": "2025-11-01T02:27:18.460724" }, "bam - stub": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -58,16 +70,20 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T15:05:56.722672" + "timestamp": "2025-11-01T02:27:30.245839" }, "cram - stub": { "content": [ @@ -82,7 +98,11 @@ ] ], "1": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -93,16 +113,20 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T15:06:13.766719" + "timestamp": "2025-11-01T02:27:39.041649" }, "bam": { "content": [ @@ -117,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -128,15 +156,19 @@ "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9" ] ], - "versions": [ - "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T15:05:30.301153" + "timestamp": "2025-11-01T02:26:55.988241" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index a5a1772b3..dcc9cec51 100644 --- a/nextflow.config +++ b/nextflow.config @@ -400,7 +400,7 @@ manifest { name: 'Eduard Casas', affiliation: 'Watchmaker Genomics', email: 'eduard.casas@watchmakergenomics.com', - github: 'https://github.com/', + github: 'https://github.com/eduard-watchmaker', contribution: ['contributor', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '0000-0002-6001-1276' ] diff --git a/nextflow_schema.json b/nextflow_schema.json index 1c3968d1f..30b5f730f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -120,7 +120,7 @@ }, "bwamem_index": { "type": "string", - "format": "file-path", + "format": "directory-path", "description": "Path to the BWA-MEM index filename base", "help_text": "Directory for a bwa-mem genome reference index. Only used when using the bwa-mem aligner.\n\nNote that this is not a complete path, but the directory containing the reference. For example, if you have file paths such as `/path/to/ref/genome.fa.bwamem.c2t.bwt`, you should specify `/path/to/ref/`.", "fa_icon": "far fa-dot-circle" diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index be814e446..bd1fc22d7 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-11-20T09:31:57+00:00", - "description": "

\n \n \n \"nf-core/methylseq\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/methylseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/methylseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/methylseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.\n\n![nf-core/methylseq metro map](docs/images/4.2.0_metromap.png)\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity / Podman / Charliecloud / Apptainer containers making installation trivial and results highly reproducible.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results).\n\n> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](docs/usage/bs-seq-primer.md)\n\n## Pipeline Summary\n\nThe pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark), [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel) or [BWA-Mem](https://github.com/lh3/bwa) plus [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/) for for TAPS data processing. rastair can also be used with bwa-meth aligned reads by setting the aligner to `--aligner bwameth` and adding the flag `--taps`.\n\nChoose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat`, `--aligner bwameth` or `--aligner bwamem`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html) and the [Parabricks implementation of bwa-mem (fq2bammemh)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html), which implement the baseline tools `bwa-meth` and `bwa-mem`. To use this option, include the `gpu` profile along with `--aligner bwameth` or `--aligner bwamem`.\n\nNote: For faster CPU runs with BWA-Meth, enable the BWA-MEM2 algorithm using `--use_mem2`. The GPU pathway (Parabricks) requires `-profile gpu` and a container runtime (Docker, Singularity, or Podman); Conda/Mamba are not supported for the GPU module.\n\n| Step | Bismark workflow | bwa-meth workflow | bwa-mem + TAPS workflow |\n| -------------------------------------------- | ------------------------ | --------------------- | -------------------------- |\n| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth | bwa index |\n| Merge re-sequenced FastQ files | cat | cat | cat |\n| Raw data QC | FastQC | FastQC | FastQC |\n| Adapter sequence trimming | Trim Galore! | Trim Galore! | Trim Galore! |\n| Align Reads | Bismark (bowtie2/hisat2) | bwa-meth | bwa mem |\n| Deduplicate Alignments | Bismark | Picard MarkDuplicates | Picard MarkDuplicates |\n| Extract methylation calls | Bismark | MethylDackel | TAPS subworkflow (rastair) |\n| Sample report | Bismark | - | - |\n| Summary Report | Bismark | - | - |\n| Alignment QC | Qualimap _(optional)_ | Qualimap _(optional)_ | Qualimap _(optional)_ |\n| Sample complexity | Preseq _(optional)_ | Preseq _(optional)_ | Preseq _(optional)_ |\n| Project Report | MultiQC | MultiQC | MultiQC |\n\nOptional targeted sequencing analysis is available via `--run_targeted_sequencing` and `--target_regions_file`; see the [usage documentation](https://nf-co.re/methylseq/usage) for details.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,genome\nSRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,\nSRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,\nSRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,\nEcoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,\n```\n\n> Each row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using default parameters as:\n\n```bash\nnextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output).\n\n## Credits\n\nnf-core/methylseq was originally written by Phil Ewels ([@ewels](https://github.com/ewels)), and Sateesh Peri ([@sateeshperi](https://github.com/sateeshperi)) is its active maintainer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))\n- Edmund Miller ([@EMiller88](https://github.com/emiller88))\n- Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn/))\n- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))\n- Patrick H\u00fcther ([@phue](https://github.com/phue/))\n- Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/))\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/methylseq\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/methylseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/methylseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/methylseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.\n\n![nf-core/methylseq metro map](docs/images/4.2.0_metromap.png)\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity / Podman / Charliecloud / Apptainer containers making installation trivial and results highly reproducible.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results).\n\n> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](docs/usage/bs-seq-primer.md)\n\n## Pipeline Summary\n\nThe pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark), [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel) or [BWA-Mem](https://github.com/lh3/bwa) plus [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/) for for TAPS data processing. rastair can also be used with bwa-meth aligned reads by setting the aligner to `--aligner bwameth` and adding the flag `--taps`.\n\nChoose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat`, `--aligner bwameth` or `--aligner bwamem`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html) and the [Parabricks implementation of bwa-mem (fq2bammemh)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html), which implement the baseline tools `bwa-meth` and `bwa-mem`. To use this option, include the `gpu` profile along with `--aligner bwameth` or `--aligner bwamem`.\n\nNote: For faster CPU runs with BWA-Meth, enable the BWA-MEM2 algorithm using `--use_mem2`. The GPU pathway (Parabricks) requires `-profile gpu` and a container runtime (Docker, Singularity, or Podman); Conda/Mamba are not supported for the GPU module.\n\n| Step | Bismark workflow | bwa-meth workflow | bwa-mem + TAPS workflow |\n| -------------------------------------------- | ------------------------ | --------------------- | -------------------------- |\n| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth | bwa index |\n| Merge re-sequenced FastQ files | cat | cat | cat |\n| Raw data QC | FastQC | FastQC | FastQC |\n| Adapter sequence trimming | Trim Galore! | Trim Galore! | Trim Galore! |\n| Align Reads | Bismark (bowtie2/hisat2) | bwa-meth | bwa mem |\n| Deduplicate Alignments | Bismark | Picard MarkDuplicates | Picard MarkDuplicates |\n| Extract methylation calls | Bismark | MethylDackel | TAPS subworkflow (rastair) |\n| Sample report | Bismark | - | - |\n| Summary Report | Bismark | - | - |\n| Alignment QC | Qualimap _(optional)_ | Qualimap _(optional)_ | Qualimap _(optional)_ |\n| Sample complexity | Preseq _(optional)_ | Preseq _(optional)_ | Preseq _(optional)_ |\n| Project Report | MultiQC | MultiQC | MultiQC |\n\nOptional targeted sequencing analysis is available via `--run_targeted_sequencing` and `--target_regions_file`; see the [usage documentation](https://nf-co.re/methylseq/usage) for details.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,genome\nSRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,\nSRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,\nSRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,\nEcoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,\n```\n\n> Each row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using default parameters as:\n\n```bash\nnextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output).\n\n## Credits\n\nnf-core/methylseq was originally written by Phil Ewels ([@ewels](https://github.com/ewels)), and Sateesh Peri ([@sateeshperi](https://github.com/sateeshperi)) is its active maintainer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))\n- Edmund Miller ([@EMiller88](https://github.com/emiller88))\n- Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn/))\n- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))\n- Patrick H\u00fcther ([@phue](https://github.com/phue/))\n- Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/))\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" diff --git a/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf index 8378b53d8..91aa65443 100644 --- a/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf @@ -167,6 +167,14 @@ workflow PIPELINE_COMPLETION { if (hook_url) { imNotification(summary_params, hook_url) } + + // Merge topic channel versions into the main versions file + // This is a workaround until all modules use topic channels + def mqcVersionsFile = file("${outdir}/pipeline_info/nf_core_methylseq_software_mqc_versions.yml") + def topicVersionsFile = file("${outdir}/pipeline_info/nf_core_methylseq_topic_versions.yml") + if (topicVersionsFile.exists() && mqcVersionsFile.exists()) { + mqcVersionsFile.append(topicVersionsFile.text) + } } workflow.onError { diff --git a/subworkflows/nf-core/bam_methyldackel/tests/main.nf.test.snap b/subworkflows/nf-core/bam_methyldackel/tests/main.nf.test.snap index be8b69859..af0c82307 100644 --- a/subworkflows/nf-core/bam_methyldackel/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_methyldackel/tests/main.nf.test.snap @@ -67,9 +67,9 @@ } ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.0", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:24:08.679423848" + "timestamp": "2025-09-18T15:04:48.063001" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index 460726368..ccef09d88 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -16,7 +16,6 @@ workflow BAM_SORT_STATS_SAMTOOLS { ch_versions = Channel.empty() SAMTOOLS_SORT ( ch_bam, ch_fasta, '' ) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index d41cc63d6..239f163c7 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -25,22 +25,20 @@ "id": "test", "single_end": false }, - "test.stats:md5,0bd81b7c8526d1c3654bf4d06600821d" + "test.stats:md5,1101fe711c4a389fdb5c4a1532107d1f" ] ], [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:24:18.955448229" + "timestamp": "2025-11-01T03:04:39.140333" }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -68,22 +66,20 @@ "id": "test", "single_end": false }, - "test.stats:md5,ef183cc74d11bbe887b2056eefc38278" + "test.stats:md5,f26c554c244ee86c89d62ebed509fd95" ] ], [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:24:29.029191256" + "timestamp": "2025-11-01T03:04:48.787289" }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -94,7 +90,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -103,7 +99,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -137,10 +133,8 @@ ] ], "6": [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], "bai": [ @@ -149,7 +143,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -158,7 +152,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "csi": [ @@ -192,19 +186,17 @@ ] ], "versions": [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:24:39.316736435" + "timestamp": "2025-11-01T03:05:00.693649" }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -215,7 +207,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -224,7 +216,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -258,10 +250,8 @@ ] ], "6": [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], "bai": [ @@ -270,7 +260,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -279,7 +269,7 @@ "id": "test", "single_end": false }, - "test.deduplicated.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "csi": [ @@ -313,18 +303,16 @@ ] ], "versions": [ - "versions.yml:md5,199b33608db0a9457645d070ab24b71b", "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", - "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:24:49.522466307" + "timestamp": "2025-11-01T03:05:10.863912" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index 44d4c010a..90fcbf80c 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -15,7 +15,6 @@ workflow BAM_STATS_SAMTOOLS { ch_versions = Channel.empty() SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) SAMTOOLS_FLAGSTAT ( ch_bam_bai ) ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index d86279630..3c543191d 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -31,8 +31,7 @@ ], "3": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ], "flagstat": [ [ @@ -63,16 +62,15 @@ ], "versions": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:25:32.202913016" + "timestamp": "2025-11-01T02:39:28.707989" }, "test_bam_stats_samtools_single_end - stub": { "content": [ @@ -106,8 +104,7 @@ ], "3": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ], "flagstat": [ [ @@ -138,16 +135,15 @@ ], "versions": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:25:23.695445241" + "timestamp": "2025-11-01T02:39:20.473816" }, "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ @@ -181,8 +177,7 @@ ], "3": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ], "flagstat": [ [ @@ -213,16 +208,15 @@ ], "versions": [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:25:40.576315411" + "timestamp": "2025-11-01T02:39:37.697552" }, "test_bam_stats_samtools_single_end": { "content": [ @@ -250,20 +244,19 @@ "id": "test", "single_end": true }, - "test.stats:md5,0bf2d071a72dd19461e8207fe50ab2bc" + "test.stats:md5,7a05a22bdb17e8df6e8c2d100ff09a31" ] ], [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:24:58.246864027" + "timestamp": "2025-11-01T02:38:50.143087" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +284,19 @@ "id": "test", "single_end": true }, - "test.stats:md5,9813b9275caee52b958bb11f94b49d6b" + "test.stats:md5,a391612b5ef5b181e854ccaad8c8a068" ] ], [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:25:06.572678034" + "timestamp": "2025-11-01T02:39:01.02311" }, "test_bam_stats_samtools_paired_end_cram": { "content": [ @@ -332,19 +324,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,c995ccd64c765c41401d650d0ff9ebc3" + "test.stats:md5,2b0e31ab01b867a6ff312023ae03838d" ] ], [ "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181", - "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa", - "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520" + "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:25:15.292458811" + "timestamp": "2025-11-01T02:39:12.503355" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_taps_conversion/tests/main.nf.test.snap b/subworkflows/nf-core/bam_taps_conversion/tests/main.nf.test.snap index a41aa8cfe..eebab1de0 100644 --- a/subworkflows/nf-core/bam_taps_conversion/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_taps_conversion/tests/main.nf.test.snap @@ -68,6 +68,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:25:53.602873723" + "timestamp": "2025-09-30T12:37:08.46254876" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_index_methylseq/main.nf b/subworkflows/nf-core/fasta_index_methylseq/main.nf index e0a7c5db4..4c74bc555 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/main.nf +++ b/subworkflows/nf-core/fasta_index_methylseq/main.nf @@ -1,4 +1,5 @@ -include { UNTAR } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_BISMARK } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_BWAMETH } from '../../../modules/nf-core/untar/main' include { GUNZIP } from '../../../modules/nf-core/gunzip/main' include { BISMARK_GENOMEPREPARATION as BISMARK_GENOMEPREPARATION_BOWTIE } from '../../../modules/nf-core/bismark/genomepreparation/main' include { BISMARK_GENOMEPREPARATION as BISMARK_GENOMEPREPARATION_HISAT } from '../../../modules/nf-core/bismark/genomepreparation/main' @@ -14,18 +15,18 @@ workflow FASTA_INDEX_METHYLSEQ { bismark_index // channel: [ val(meta), [ bismark index ] ] bwameth_index // channel: [ val(meta), [ bwameth index ] ] bwamem_index // channel: [ val(meta), [ bwamem index ] ] - aligner // string: bismark, bismark_hisat or bwameth + aligner // string: bismark, bismark_hisat, bwameth or bwamem collecthsmetrics // boolean: whether to run picard collecthsmetrics use_mem2 // boolean: generate mem2 index if no index provided, and bwameth is selected main: - ch_fasta = Channel.empty() - ch_fasta_index = Channel.empty() - ch_bismark_index = Channel.empty() - ch_bwameth_index = Channel.empty() - ch_bwamem_index = Channel.empty() - ch_versions = Channel.empty() + ch_fasta = channel.empty() + ch_fasta_index = channel.empty() + ch_bismark_index = channel.empty() + ch_bwameth_index = channel.empty() + ch_bwamem_index = channel.empty() + ch_versions = channel.empty() // Check if fasta file is gzipped and decompress if needed fasta @@ -56,17 +57,17 @@ workflow FASTA_INDEX_METHYLSEQ { } .set { ch_bismark_index_branched } - UNTAR ( + UNTAR_BISMARK ( ch_bismark_index_branched.gzipped ) - ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR.out.untar) - ch_versions = ch_versions.mix(UNTAR.out.versions) + ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) + ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { if( aligner == "bismark_hisat") { BISMARK_GENOMEPREPARATION_HISAT ( - ch_fasta + ch_fasta ) ch_bismark_index = BISMARK_GENOMEPREPARATION_HISAT.out.index ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION_HISAT.out.versions) @@ -94,24 +95,17 @@ workflow FASTA_INDEX_METHYLSEQ { } .set { ch_bwameth_index_branched } - UNTAR ( + UNTAR_BWAMETH ( ch_bwameth_index_branched.gzipped ) - ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR.out.untar) - ch_versions = ch_versions.mix(UNTAR.out.versions) + ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR_BWAMETH.out.untar) + ch_versions = ch_versions.mix(UNTAR_BWAMETH.out.versions) } else { - if (use_mem2) { - BWAMETH_INDEX ( - ch_fasta, - true - ) - } else { - BWAMETH_INDEX ( - ch_fasta, - false - ) - } + BWAMETH_INDEX ( + ch_fasta, + use_mem2 + ) ch_bwameth_index = BWAMETH_INDEX.out.index ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions) } @@ -119,14 +113,27 @@ workflow FASTA_INDEX_METHYLSEQ { else if ( aligner == 'bwamem' ){ - log.info "BWA index not provided. Generating BWA index from FASTA file." /* * Generate BWA index from FASTA file */ if (bwamem_index) { - ch_bwamem_index = bwamem_index + // Handle channel-based bwamem index + bwamem_index + .branch { + gzipped: it[1].toString().endsWith('.gz') + unzipped: true + } + .set { ch_bwamem_index_branched } + + UNTAR_BISMARK ( + ch_bwamem_index_branched.gzipped + ) + + ch_bwamem_index = ch_bwamem_index_branched.unzipped.mix(UNTAR_BISMARK.out.untar) + ch_versions = ch_versions.mix(UNTAR_BISMARK.out.versions) } else { - BWA_INDEX( + log.info "BWA index not provided. Generating BWA index from FASTA file." + BWA_INDEX ( ch_fasta ) ch_bwamem_index = BWA_INDEX.out.index @@ -138,11 +145,12 @@ workflow FASTA_INDEX_METHYLSEQ { * Generate fasta index if not supplied for bwameth workflow or picard collecthsmetrics tool */ if (aligner == 'bwameth' || aligner == 'bwamem' || collecthsmetrics) { - // already exising fasta index + // already existing fasta index if (fasta_index) { ch_fasta_index = fasta_index } else { - SAMTOOLS_FAIDX( + log.info "Fasta index not provided. Generating fasta index from FASTA file." + SAMTOOLS_FAIDX ( ch_fasta, [[:], []], false @@ -157,6 +165,6 @@ workflow FASTA_INDEX_METHYLSEQ { fasta_index = ch_fasta_index // channel: [ val(meta), [ fasta index ] ] bismark_index = ch_bismark_index // channel: [ val(meta), [ bismark index ] ] bwameth_index = ch_bwameth_index // channel: [ val(meta), [ bwameth index ] ] - bwamem_index = ch_bwamem_index // channel: [ val(meta), [ bwamem index ] ] + bwamem_index = ch_bwamem_index // channel: [ val(meta), [ bwamem index ] ] versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fasta_index_methylseq/meta.yml b/subworkflows/nf-core/fasta_index_methylseq/meta.yml index cffb6cb3a..db17e8148 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/meta.yml +++ b/subworkflows/nf-core/fasta_index_methylseq/meta.yml @@ -45,7 +45,7 @@ input: - aligner: type: string description: | - Aligner name (bismark, bismark_hisat, or bwameth) + Aligner name (bismark, bismark_hisat, bwameth, or bwamem) - collecthsmetrics: type: boolean description: | diff --git a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap index 9436dc637..413870ba1 100644 --- a/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_index_methylseq/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:30:06.002892488" + "timestamp": "2025-09-30T10:55:30.325705625" }, "Params: bwameth | generate fasta index | download bwameth index": { "content": [ @@ -90,15 +90,15 @@ ], [ "versions.yml:md5,1a7e59286a0e918ba2400750ddefd444", - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:28:58.338247137" + "timestamp": "2025-12-03T12:20:26.495603" }, "Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": { "content": [ @@ -142,15 +142,15 @@ ], [ "versions.yml:md5,1a7e59286a0e918ba2400750ddefd444", - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:29:37.653724166" + "timestamp": "2025-12-03T12:21:13.279634" }, "Params: bwameth | generate fasta index | generate bwameth mem2 index": { "content": [ @@ -201,7 +201,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:29:28.22041465" + "timestamp": "2025-09-30T10:55:03.085892754" }, "Params: bismark | download bismark index (bowtie2)": { "content": [ @@ -253,15 +253,15 @@ ], [ - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", - "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" + "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97", + "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:27:58.991145888" + "timestamp": "2025-12-03T12:19:16.006311" }, "Params: bwameth | generate fasta index | download bwameth mem2 index | collecthsmetrics": { "content": [ @@ -304,15 +304,15 @@ ], [ "versions.yml:md5,1a7e59286a0e918ba2400750ddefd444", - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:29:47.265796536" + "timestamp": "2025-12-03T12:21:24.368005" }, "Params: bwameth | generate fasta index | download bwameth mem2 index": { "content": [ @@ -355,15 +355,15 @@ ], [ "versions.yml:md5,1a7e59286a0e918ba2400750ddefd444", - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:29:07.909994921" + "timestamp": "2025-12-03T12:20:37.640088" }, "Params: bwameth | generate fasta index | generate bwameth index": { "content": [ @@ -414,7 +414,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:29:17.685324552" + "timestamp": "2025-09-30T10:54:55.205128637" }, "Params: bismark_hisat | generate bismark index (hisat2)": { "content": [ @@ -470,15 +470,15 @@ ], [ - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", - "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" + "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97", + "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:28:31.27723812" + "timestamp": "2025-12-03T12:19:53.905574" }, "Params: bismark_hisat | download bismark index (hisat2)": { "content": [ @@ -534,15 +534,15 @@ ], [ - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", - "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" + "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97", + "versions.yml:md5,d3ed85f31ec769229e17780530e235ee" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:28:22.34377813" + "timestamp": "2025-12-03T12:19:42.978899" }, "Params: bwameth | download fasta index | download bwameth index": { "content": [ @@ -585,15 +585,15 @@ ], [ - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:28:40.273456165" + "timestamp": "2025-12-03T12:20:04.798139" }, "Params: bwameth | download fasta index | download bwameth mem2 index": { "content": [ @@ -635,15 +635,15 @@ ], [ - "versions.yml:md5,80527e72159961c33cd9a6d4847e75e3", + "versions.yml:md5,51df3ff0a3067a7a676cdc4e4d237a69", "versions.yml:md5,8afe74b43d9155c93e27ae1b36a7ae97" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:28:48.948079654" + "timestamp": "2025-12-03T12:20:15.282566" }, "Params: bwamem | generate fasta index | generate bwamem index": { "content": [ @@ -693,7 +693,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-10-21T22:29:56.687795749" + "timestamp": "2025-09-30T10:55:23.700638588" }, "Params: bismark | generate bismark index (bowtie2)": { "content": [ @@ -751,8 +751,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-10-21T22:28:13.532582524" + "timestamp": "2025-09-30T15:20:44.974184664" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap index e0bc205a1..26866be14 100644 --- a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,775a9eeb05ed2eba44e7951d67dba939" + "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" ] ], "1": [ @@ -17,7 +17,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,3b6ab22f3675df42fd8dea7c9099eafd" + "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" ] ], "2": [ @@ -26,7 +26,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,70bc529b1d153fd64aa4eec9a79310fb" + "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" ] ], "3": [ @@ -38,7 +38,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,a29aebbeb63e88fbfdb43ed0792e3dd1" + "test.sorted.bam.stats:md5,75934f2a51780a80d2ab4674301a018d" ] ], "5": [ @@ -63,9 +63,7 @@ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,a8c41baee5c473ada025c29ebb5c06e0", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9", - "versions.yml:md5,e83f9eaf352590ab72d4dbd4699dd1c0" + "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ], "bai": [ [ @@ -73,7 +71,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,70bc529b1d153fd64aa4eec9a79310fb" + "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" ] ], "bam": [ @@ -82,7 +80,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,3b6ab22f3675df42fd8dea7c9099eafd" + "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" ] ], "bam_orig": [ @@ -91,7 +89,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,775a9eeb05ed2eba44e7951d67dba939" + "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" ] ], "csi": [ @@ -121,24 +119,22 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,a29aebbeb63e88fbfdb43ed0792e3dd1" + "test.sorted.bam.stats:md5,75934f2a51780a80d2ab4674301a018d" ] ], "versions": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,a8c41baee5c473ada025c29ebb5c06e0", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9", - "versions.yml:md5,e83f9eaf352590ab72d4dbd4699dd1c0" + "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-10-21T22:30:31.004339684" + "timestamp": "2025-11-26T13:43:05.771242" }, "fastq_align_bwa_single_end": { "content": [ @@ -149,7 +145,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,c95661e8cbdda275ecbfe92f65fd38e0" + "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" ] ], "1": [ @@ -158,7 +154,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,1d109d4840242560a9bf1820f4e1c38e" + "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" ] ], "2": [ @@ -179,7 +175,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam.stats:md5,4e6327473c28fe17f886e6f6023b0de9" + "test.sorted.bam.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" ] ], "5": [ @@ -204,9 +200,7 @@ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,a8c41baee5c473ada025c29ebb5c06e0", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9", - "versions.yml:md5,e83f9eaf352590ab72d4dbd4699dd1c0" + "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ], "bai": [ [ @@ -223,7 +217,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,1d109d4840242560a9bf1820f4e1c38e" + "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" ] ], "bam_orig": [ @@ -232,7 +226,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,c95661e8cbdda275ecbfe92f65fd38e0" + "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" ] ], "csi": [ @@ -262,23 +256,21 @@ "id": "test", "single_end": true }, - "test.sorted.bam.stats:md5,4e6327473c28fe17f886e6f6023b0de9" + "test.sorted.bam.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" ] ], "versions": [ "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,a8c41baee5c473ada025c29ebb5c06e0", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9", - "versions.yml:md5,e83f9eaf352590ab72d4dbd4699dd1c0" + "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-10-21T22:30:18.45447224" + "timestamp": "2025-11-26T13:42:37.663363" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf index 7708fb2f8..c08686cb5 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf @@ -17,20 +17,20 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { cytosine_report // boolean: whether the run coverage2cytosine main: - ch_alignments = Channel.empty() - ch_alignment_reports = Channel.empty() - ch_methylation_bedgraph = Channel.empty() - ch_methylation_calls = Channel.empty() - ch_methylation_coverage = Channel.empty() - ch_methylation_report = Channel.empty() - ch_methylation_mbias = Channel.empty() - ch_coverage2cytosine_coverage = Channel.empty() - ch_coverage2cytosine_report = Channel.empty() - ch_coverage2cytosine_summary = Channel.empty() - ch_bismark_report = Channel.empty() - ch_bismark_summary = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_versions = Channel.empty() + ch_alignments = channel.empty() + ch_alignment_reports = channel.empty() + ch_methylation_bedgraph = channel.empty() + ch_methylation_calls = channel.empty() + ch_methylation_coverage = channel.empty() + ch_methylation_report = channel.empty() + ch_methylation_mbias = channel.empty() + ch_coverage2cytosine_coverage = channel.empty() + ch_coverage2cytosine_report = channel.empty() + ch_coverage2cytosine_summary = channel.empty() + ch_bismark_report = channel.empty() + ch_bismark_summary = channel.empty() + ch_multiqc_files = channel.empty() + ch_versions = channel.empty() /* * Align with bismark @@ -42,7 +42,6 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { ) ch_alignments = BISMARK_ALIGN.out.bam ch_alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } - ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) if (!skip_deduplication) { /* @@ -64,7 +63,6 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { [[:],[]], // [ [meta], [fasta]] '' ) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) /* * MODULE: Run samtools index on aligned or deduplicated bam @@ -118,11 +116,11 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { * Generate bismark summary report */ BISMARK_SUMMARY ( - BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam.name }, - ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }, - ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]), - ch_methylation_report.collect{ meta, report -> report }, - ch_methylation_mbias.collect{ meta, mbias -> mbias } + BISMARK_ALIGN.out.bam.collect{ _meta, bam -> bam.name }, + ch_alignment_reports.collect{ _meta, align_report, _dedup_report -> align_report }, + ch_alignment_reports.collect{ _meta, _align_report, dedup_report -> dedup_report }.ifEmpty([]), + ch_methylation_report.collect{ _meta, report -> report }, + ch_methylation_mbias.collect{ _meta, mbias -> mbias } ) ch_bismark_summary = BISMARK_SUMMARY.out.summary ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) @@ -131,11 +129,11 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { * Collect MultiQC inputs */ ch_multiqc_files = ch_bismark_summary - .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }) - .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }) - .mix(ch_methylation_report.collect{ meta, report -> report }) - .mix(ch_methylation_mbias.collect{ meta, mbias -> mbias }) - .mix(ch_bismark_report.collect{ meta, report -> report }) + .mix(ch_alignment_reports.collect{ _meta, align_report, _dedup_report -> align_report }) + .mix(ch_alignment_reports.collect{ _meta, _align_report, dedup_report -> dedup_report }) + .mix(ch_methylation_report.collect{ _meta, report -> report }) + .mix(ch_methylation_mbias.collect{ _meta, mbias -> mbias }) + .mix(ch_bismark_report.collect{ _meta, report -> report }) emit: bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml index 7622b98e8..9c31668b6 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml @@ -121,9 +121,9 @@ output: - multiqc: type: file description: | - Channel containing MultiQC report aggregating results across samples. - Structure: [ val(meta), path(multiqc_report.html) ] - pattern: "*.html" + Channel containing files for MultiQC input (reports, alignment reports, methylation reports). + Structure: [ path(files) ] + pattern: "*.{html,txt}" - versions: type: file description: | diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test index 27bf692af..41a18cd17 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test @@ -105,9 +105,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], @@ -154,9 +156,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], @@ -203,9 +207,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], @@ -302,9 +308,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], @@ -351,9 +359,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], @@ -400,9 +410,11 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + [ id:'test', single_end:false ], + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ] ]) input[1] = Channel.of([ [:], diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap index acb784059..3067314ee 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "Params: bismark_hisat paired-end | default": { "content": [ [ - "4bf31467bec7b5d5669aa4ac16f6f93f" + "37b8bb55cd310598c52a7b1376c538b8" ], [ "test.sorted.bam.bai" @@ -20,24 +20,24 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.bedGraph.gz:md5,036f675959865a43f49899108d53b546" + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,bbaf7200b30dd78f578df81c65aa3b12" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,d01f69d7783908ae35cfb80dba5d7177", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,ce1d1bdf2179a3280f8a2127e6ea6c7f", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,7d094368fc3b95cdbb45e818b7c3119f", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,3b90716df9726fac04f7ab52d0ff4de4", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,6d6e0d34e79e36d205699a3f91316b21", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.txt.gz:md5,b1ba62c4e7fb33fe4e35d203a0814552" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,275586e525fa8026af3945b6fd372807", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,d15db39c712f65679cce464da6152f72", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,c860eff2055ebfa5ab51eaa74c844b1a", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,e216e668a80eb0af621ea28bf30649a4", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,ceed6d29a4364cf820ff8c5e583b207a", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" ] ] ], @@ -45,62 +45,60 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.bismark.cov.gz:md5,63511c46275713088957950285acd653" + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,1b7b806b845ac9881c655ea7ab29ef2a" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated_splitting_report.txt:md5,ba02f4b97aa69b1ee1a0df5b06e34472" + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,56456b46726a6c7123ce9b47be410f8e" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.M-bias.txt:md5,857b28589351f2c63f587a2c040db748" + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,1cdd6bb3f7d6ac41a60a5312245cfb0a" ] ], [ - "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.html" + "Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html" ], - "bismark_summary_report.txt:md5,9f62c10d005c39d3e5ee7961b6b0bf6b", + "bismark_summary_report.txt:md5,70e16c0041dfbf255b70d1eb60df5c54", [ - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated.M-bias.txt", - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplicated_splitting_report.txt", - "Ecoli_10K_methylated_R1_bismark_hisat2.deduplication_report.txt", - 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"timestamp": "2025-10-21T22:33:42.661825669" + "timestamp": "2025-12-03T12:54:08.096501" }, "Params: bismark paired-end | default": { "content": [ [ - "4bf31467bec7b5d5669aa4ac16f6f93f" + "b49754b06cf7a7fc8d31b973e5ee9cc3" ], [ "test.sorted.bam.bai" @@ -118,24 +116,24 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.bedGraph.gz:md5,036f675959865a43f49899108d53b546" + "Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,7262545b878b2c685d83566d94ab7622" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,d01f69d7783908ae35cfb80dba5d7177", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,ce1d1bdf2179a3280f8a2127e6ea6c7f", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,7d094368fc3b95cdbb45e818b7c3119f", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,3b90716df9726fac04f7ab52d0ff4de4", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,6d6e0d34e79e36d205699a3f91316b21", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.txt.gz:md5,b1ba62c4e7fb33fe4e35d203a0814552" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,a5315ec249edb9e90d04c8cd79574eb6", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,d15db39c712f65679cce464da6152f72", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,db9ef72b9f85ac7d0a0b70798b6b05a5", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,e216e668a80eb0af621ea28bf30649a4", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,eab3936aeadb93309dc853b911446969", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" ] ] ], @@ -143,57 +141,55 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.bismark.cov.gz:md5,63511c46275713088957950285acd653" + "Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,589bf81db14b3464a7fde598ef8bb3c3" ] ], [ [ { "id": "test", - 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"Ecoli_10K_methylated_R1_bismark_hisat2.M-bias.txt", - "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.html", - "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.txt", - "Ecoli_10K_methylated_R1_bismark_hisat2_splitting_report.txt", + "Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html", + "Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt", "bismark_summary_report.html", "bismark_summary_report.txt" ], [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", - "versions.yml:md5,4c4034ba26cdbb854bdaca244fbe7753", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99", - "versions.yml:md5,c46e760b8c68f4c6037d2c60d12c06f9" + "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:34:11.515760853" + "timestamp": "2025-12-03T12:54:41.001127" }, "Params: bismark paired-end | skip_deduplication": { "content": [ [ - "4bf31467bec7b5d5669aa4ac16f6f93f" + "b49754b06cf7a7fc8d31b973e5ee9cc3" ], [ "test.sorted.bam.bai" @@ -632,24 +620,24 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2.bedGraph.gz:md5,036f675959865a43f49899108d53b546" + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,7262545b878b2c685d83566d94ab7622" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,d01f69d7783908ae35cfb80dba5d7177", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,ce1d1bdf2179a3280f8a2127e6ea6c7f", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,7d094368fc3b95cdbb45e818b7c3119f", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,3b90716df9726fac04f7ab52d0ff4de4", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,6d6e0d34e79e36d205699a3f91316b21", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,b1ba62c4e7fb33fe4e35d203a0814552" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,a5315ec249edb9e90d04c8cd79574eb6", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,d15db39c712f65679cce464da6152f72", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,db9ef72b9f85ac7d0a0b70798b6b05a5", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,e216e668a80eb0af621ea28bf30649a4", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,eab3936aeadb93309dc853b911446969", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" ] ] ], @@ -657,55 +645,53 @@ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2.bismark.cov.gz:md5,63511c46275713088957950285acd653" + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz:md5,589bf81db14b3464a7fde598ef8bb3c3" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2_splitting_report.txt:md5,7e8d03d9dce62c62a9fe1703e22022e9" + "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt:md5,d827deca8065fce65c814bf09a15ba92" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, - "Ecoli_10K_methylated_R1_bismark_bt2.M-bias.txt:md5,857b28589351f2c63f587a2c040db748" + "Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt:md5,9cb860148c032fe23e520323b3aa6610" ] ], [ - "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html" + "Ecoli_10K_methylated_R1_bismark_bt2_PE_report.html" ], - "bismark_summary_report.txt:md5,9f639cca6fe43c0461d2da88d931a036", + "bismark_summary_report.txt:md5,87d0db5195a75381dec2f2809daa0b45", [ - "Ecoli_10K_methylated_R1_bismark_bt2.M-bias.txt", - "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html", - "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.txt", - "Ecoli_10K_methylated_R1_bismark_bt2_splitting_report.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_PE_report.html", + "Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt", "bismark_summary_report.html", "bismark_summary_report.txt" ], [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", - "versions.yml:md5,4c4034ba26cdbb854bdaca244fbe7753", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99", - "versions.yml:md5,c46e760b8c68f4c6037d2c60d12c06f9" + "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:32:05.426587379" + "timestamp": "2025-12-03T12:52:19.185514" }, "Params: bismark_hisat single-end | default": { "content": [ @@ -791,18 +777,16 @@ ], [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", - "versions.yml:md5,4c4034ba26cdbb854bdaca244fbe7753", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99", - "versions.yml:md5,c46e760b8c68f4c6037d2c60d12c06f9" + "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-21T22:33:13.05514377" + "timestamp": "2025-11-26T16:08:32.039526" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf index a496e1e3b..026bbf6f7 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf @@ -1,7 +1,7 @@ -include { FASTQ_ALIGN_BWA } from '../fastq_align_bwa/main' -include { PICARD_ADDORREPLACEREADGROUPS } from '../../../modules/nf-core/picard/addorreplacereadgroups/main' -include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { FASTQ_ALIGN_BWA } from '../fastq_align_bwa/main' +include { PICARD_ADDORREPLACEREADGROUPS } from '../../../modules/nf-core/picard/addorreplacereadgroups/main' +include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' workflow FASTQ_ALIGN_DEDUP_BWAMEM { @@ -9,19 +9,18 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { ch_reads // channel: [ val(meta), [ reads ] ] ch_fasta // channel: [ val(meta), [ fasta ] ] ch_fasta_index // channel: [ val(meta), [ fasta index ] ] - ch_bwamem_index // channel: [ val(meta), [ bwam index ] ] + ch_bwamem_index // channel: [ val(meta), [ bwamem index ] ] skip_deduplication // boolean: whether to deduplicate alignments - use_gpu // boolean: whether to use GPU or CPU for bwamem alignment main: - - ch_alignment = Channel.empty() - ch_alignment_index = Channel.empty() - ch_flagstat = Channel.empty() - ch_stats = Channel.empty() - ch_picard_metrics = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_versions = Channel.empty() + ch_alignment = channel.empty() + ch_alignment_index = channel.empty() + ch_flagstat = channel.empty() + ch_stats = channel.empty() + ch_idxstats = channel.empty() + ch_picard_metrics = channel.empty() + ch_multiqc_files = channel.empty() + ch_versions = channel.empty() FASTQ_ALIGN_BWA ( ch_reads, @@ -29,11 +28,11 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { true, // val_sort_bam hardcoded to true ch_fasta ) - ch_alignment = ch_alignment.mix(FASTQ_ALIGN_BWA.out.bam) - ch_alignment_index = ch_alignment.mix(FASTQ_ALIGN_BWA.out.bai) - ch_stats = ch_alignment.mix(FASTQ_ALIGN_BWA.out.stats) // channel: [ val(meta), path(stats) ] - ch_flagstat = ch_alignment.mix(FASTQ_ALIGN_BWA.out.flagstat) // channel: [ val(meta), path(flagstat) ] - ch_idxstats = ch_alignment.mix(FASTQ_ALIGN_BWA.out.idxstats) // channel: [ val(meta), path(idxstats) ] + ch_alignment = FASTQ_ALIGN_BWA.out.bam // channel: [ val(meta), [ bam ] ] + ch_alignment_index = FASTQ_ALIGN_BWA.out.bai // channel: [ val(meta), [ bai ] ] + ch_stats = FASTQ_ALIGN_BWA.out.stats // channel: [ val(meta), path(stats) ] + ch_flagstat = FASTQ_ALIGN_BWA.out.flagstat // channel: [ val(meta), path(flagstat) ] + ch_idxstats = FASTQ_ALIGN_BWA.out.idxstats // channel: [ val(meta), path(idxstats) ] ch_versions = ch_versions.mix(FASTQ_ALIGN_BWA.out.versions.first()) if (!skip_deduplication) { @@ -48,9 +47,8 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS.out.versions.first()) /* - * Run Picard MarkDuplicates with the --REMOVE_DUPLICATES true flag + * Run Picard MarkDuplicates to mark duplicates */ - PICARD_MARKDUPLICATES ( PICARD_ADDORREPLACEREADGROUPS.out.bam, ch_fasta, @@ -73,18 +71,18 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { /* * Collect MultiQC inputs */ - ch_multiqc_files = ch_picard_metrics.collect{ meta, metrics -> metrics } - .mix(ch_flagstat.collect{ meta, flagstat -> flagstat }) - .mix(ch_stats.collect{ meta, stats -> stats }) - .mix(ch_idxstats.collect{ meta, stats -> stats }) + ch_multiqc_files = ch_picard_metrics.collect{ _meta, metrics -> metrics } + .mix(ch_flagstat.collect{ _meta, flagstat -> flagstat }) + .mix(ch_stats.collect{ _meta, stats -> stats }) + .mix(ch_idxstats.collect{ _meta, stats -> stats }) emit: - bam = ch_alignment // channel: [ val(meta), [ bam ] ] - bai = ch_alignment_index // channel: [ val(meta), [ bai ] ] - samtools_flagstat = ch_flagstat // channel: [ val(meta), [ flagstat ] ] - samtools_stats = ch_stats // channel: [ val(meta), [ stats ] ] - samtools_index_stats = ch_idxstats // channel: [ val(meta), [ idxstats ] ] - picard_metrics = ch_picard_metrics // channel: [ val(meta), [ metrics ] ] - multiqc = ch_multiqc_files // channel: [ *{html,txt} ] - versions = ch_versions // channel: [ versions.yml ] -} \ No newline at end of file + bam = ch_alignment // channel: [ val(meta), [ bam ] ] + bai = ch_alignment_index // channel: [ val(meta), [ bai ] ] + samtools_flagstat = ch_flagstat // channel: [ val(meta), [ flagstat ] ] + samtools_stats = ch_stats // channel: [ val(meta), [ stats ] ] + samtools_idxstats = ch_idxstats // channel: [ val(meta), [ idxstats ] ] + picard_metrics = ch_picard_metrics // channel: [ val(meta), [ metrics ] ] + multiqc = ch_multiqc_files // channel: [ *{html,txt} ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml index 359f2db66..fd6670e2a 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/meta.yml @@ -1,96 +1,96 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "fastq_align_dedup_bwamem" -description: Performs alignment of DNA or TAPS-treated reads using bwamem, sort and deduplicate -keywords: - - bwamem - - alignment - - map - - 5mC - - methylseq - - DNA - - fastq - - bam -components: - - samtools/index - - picard/addorreplacereadgroups - - picard/markduplicates - - fastq_align_bwa -input: - - ch_reads: - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - Structure: [ val(meta), [ path(reads) ] ] - pattern: "*.{fastq,fastq.gz}" - - ch_fasta: - type: file - description: | - Structure: [ val(meta), path(fasta) ] - pattern: "*.{fa,fa.gz}" - - ch_fasta_index: - type: file - description: | - Structure: [ val(meta), path(fasta index) ] - - ch_bwamem_index: - type: directory - description: | - Bwa-mem genome index files - Structure: [ val(meta), path(index) ] - pattern: "Bwa-memIndex" - - skip_deduplication: - type: boolean - description: | - Skip deduplication of aligned reads -output: - - bam: - type: file - description: | - Channel containing BAM files - Structure: [ val(meta), path(bam) ] - pattern: "*.bam" - - bai: - type: file - description: | - Channel containing indexed BAM (BAI) files - Structure: [ val(meta), path(bai) ] - pattern: "*.bai" - - samtools_flagstat: - type: file - description: | - File containing samtools flagstat output - Structure: [ val(meta), path(flagstat) ] - pattern: "*.flagstat" - - samtools_idxstats: - type: file - description: | - File containing samtools idxstats output - Structure: [ val(meta), path(idxstats) ] - pattern: "*.idxstats" - - samtools_stats: - type: file - description: | - File containing samtools stats output - Structure: [ val(meta), path(stats) ] - pattern: "*.{stats}" - - picard_metrics: - type: file - description: | - Duplicate metrics file generated by picard - Structure: [ val(meta), path(metrics) ] - pattern: "*.{metrics.txt}" - - multiqc: - type: file - description: | - Channel containing MultiQC report aggregating results across samples. - Structure: [ val(meta), path(multiqc_report.html) ] - pattern: "*.html" - - versions: - type: file - description: | - File containing software versions - Structure: [ path(versions.yml) ] - pattern: "versions.yml" -authors: - - "@eduard-watchmaker" -maintainers: - - "@eduard-watchmaker" \ No newline at end of file +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fastq_align_dedup_bwamem" +description: Performs alignment of DNA or TAPS-treated reads using bwamem, sort and deduplicate +keywords: + - bwamem + - alignment + - map + - 5mC + - methylseq + - DNA + - fastq + - bam +components: + - samtools/index + - picard/addorreplacereadgroups + - picard/markduplicates + - fastq_align_bwa +input: + - ch_reads: + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + Structure: [ val(meta), [ path(reads) ] ] + pattern: "*.{fastq,fastq.gz}" + - ch_fasta: + type: file + description: | + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa,fa.gz}" + - ch_fasta_index: + type: file + description: | + Structure: [ val(meta), path(fasta index) ] + - ch_bwamem_index: + type: directory + description: | + Bwa-mem genome index files + Structure: [ val(meta), path(index) ] + pattern: "Bwa-memIndex" + - skip_deduplication: + type: boolean + description: | + Skip deduplication of aligned reads +output: + - bam: + type: file + description: | + Channel containing BAM files + Structure: [ val(meta), path(bam) ] + pattern: "*.bam" + - bai: + type: file + description: | + Channel containing indexed BAM (BAI) files + Structure: [ val(meta), path(bai) ] + pattern: "*.bai" + - samtools_flagstat: + type: file + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + pattern: "*.flagstat" + - samtools_idxstats: + type: file + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats) ] + pattern: "*.idxstats" + - samtools_stats: + type: file + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + pattern: "*.{stats}" + - picard_metrics: + type: file + description: | + Duplicate metrics file generated by picard + Structure: [ val(meta), path(metrics) ] + pattern: "*.{metrics.txt}" + - multiqc: + type: file + description: | + Channel containing files for MultiQC input (metrics, stats, flagstat, idxstats). + Structure: [ path(file) ] + pattern: "*{.txt,.stats,.flagstat,.idxstats}" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@eduard-watchmaker" +maintainers: + - "@eduard-watchmaker" diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config index bb6c76659..bc1fcf151 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/nextflow.config @@ -1,13 +1,13 @@ // IMPORTANT: This config file should be included to ensure that the subworkflow works properly. process { - withName: '.*FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_SORT' { + withName: 'SAMTOOLS_SORT' { ext.prefix = { "${meta.id}.sorted" } } - withName: '.*FASTQ_ALIGN_DEDUP_BWAMEM:PICARD_MARKDUPLICATES' { + withName: 'PICARD_MARKDUPLICATES' { ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" ext.prefix = { "${meta.id}.deduped.sorted" } } - withName: '.*FASTQ_ALIGN_DEDUP_BWAMEM:PICARD_ADDORREPLACEREADGROUPS' { + withName: 'PICARD_ADDORREPLACEREADGROUPS' { ext.args = "--RGID 1 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM sample1" ext.prefix = { "${meta.id}.RG.sorted" } } diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test index f8cd922d4..56c996c5c 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_workflow { script "../../../../modules/nf-core/bwa/index/main.nf" process { """ - input[0] = [ + input[0] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -57,9 +57,6 @@ nextflow_workflow { ]) input[3] = BWA_INDEX.out.index input[4] = false // skip_deduplication - input[5] = false // use_gpu - input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites """ } } @@ -72,7 +69,7 @@ nextflow_workflow { workflow.out.bai.collect { meta, bai -> file(bai).name }, workflow.out.samtools_flagstat, workflow.out.samtools_stats, - workflow.out.samtools_index_stats, + workflow.out.samtools_idxstats, workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, workflow.out.multiqc.flatten().collect { path -> file(path).name }, workflow.out.versions @@ -88,7 +85,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], + [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]) @@ -102,9 +99,6 @@ nextflow_workflow { ]) input[3] = BWA_INDEX.out.index input[4] = false // skip_deduplication - input[5] = false // use_gpu - input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites """ } } @@ -117,7 +111,7 @@ nextflow_workflow { workflow.out.bai.collect { meta, bai -> file(bai).name }, workflow.out.samtools_flagstat, workflow.out.samtools_stats, - workflow.out.samtools_index_stats, + workflow.out.samtools_idxstats, workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, workflow.out.multiqc.flatten().collect { path -> file(path).name }, workflow.out.versions @@ -133,7 +127,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], + [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]) @@ -147,9 +141,6 @@ nextflow_workflow { ]) input[3] = BWA_INDEX.out.index input[4] = true // skip_deduplication - input[5] = false // use_gpu - input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites """ } } @@ -162,7 +153,7 @@ nextflow_workflow { workflow.out.bai.collect { meta, bai -> file(bai).name }, workflow.out.samtools_flagstat, workflow.out.samtools_stats, - workflow.out.samtools_index_stats, + workflow.out.samtools_idxstats, workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, workflow.out.multiqc.flatten().collect { path -> file(path).name }, workflow.out.versions @@ -191,9 +182,6 @@ nextflow_workflow { ]) input[3] = BWA_INDEX.out.index input[4] = false // skip_deduplication - input[5] = false // use_gpu - input[6] = [[:], [] ] // interval_file - input[7] = [[:], [] ] // known_sites """ } } @@ -201,7 +189,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( + { assert snapshot( workflow.out, workflow.out.versions.collect{ path(it).yaml } ).match() } diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap index 6d6f42b8f..5ee3a0738 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap @@ -14,13 +14,6 @@ "single_end": true }, "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ @@ -29,14 +22,7 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.stats:md5,4e6327473c28fe17f886e6f6023b0de9" + "test.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" ] ], [ @@ -46,13 +32,6 @@ "single_end": true }, "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ @@ -60,11 +39,8 @@ ], [ "test.deduped.sorted.MarkDuplicates.metrics.txt", - "test.sorted.bam", "test.flagstat", - "test.sorted.bam", "test.idxstats", - "test.sorted.bam", "test.stats" ], [ @@ -75,10 +51,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-30T16:07:31.456069727" + "timestamp": "2025-12-03T12:27:38.204299" }, "Params: bwamem paired-end - skip_deduplication": { "content": [ @@ -86,66 +62,41 @@ "94fcf617f5b994584c4e8d4044e16b4f" ], [ - "test.sorted.bam", "test.sorted.bam.bai" ], [ [ { "id": "test", - "single_end": true + "single_end": false }, "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ [ { "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" - ], - [ - { - "id": "test", - "single_end": true + "single_end": false }, - "test.stats:md5,4e6327473c28fe17f886e6f6023b0de9" + "test.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ ], [ - "test.sorted.bam", "test.flagstat", - "test.sorted.bam", "test.idxstats", - "test.sorted.bam", "test.stats" ], [ @@ -153,10 +104,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-30T16:08:02.800594333" + "timestamp": "2025-12-03T12:28:09.085652" }, "Params: bwamem single-end - default - stub": { "content": [ @@ -186,23 +137,9 @@ "single_end": true }, "test.flagstat:md5,67394650dbae96d1a4fcc70484822159" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], [ { "id": "test", @@ -218,13 +155,6 @@ "single_end": true }, "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ @@ -241,15 +171,12 @@ "test.deduped.sorted.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.flagstat:md5,67394650dbae96d1a4fcc70484822159" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], @@ -282,15 +209,12 @@ "test.deduped.sorted.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.flagstat:md5,67394650dbae96d1a4fcc70484822159" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], @@ -310,39 +234,18 @@ "single_end": true }, "test.flagstat:md5,67394650dbae96d1a4fcc70484822159" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "samtools_index_stats": [ + "samtools_idxstats": [ [ { "id": "test", "single_end": true }, "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "samtools_stats": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], [ { "id": "test", @@ -383,10 +286,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-30T16:08:18.950324064" + "timestamp": "2025-12-03T12:28:25.358403" }, "Params: bwamem paired-end - default": { "content": [ @@ -400,48 +303,27 @@ [ { "id": "test", - "single_end": true + "single_end": false }, "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ [ { "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" - ], - [ - { - "id": "test", - "single_end": true + "single_end": false }, - "test.stats:md5,4e6327473c28fe17f886e6f6023b0de9" + "test.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" ] ], [ [ { "id": "test", - "single_end": true + "single_end": false }, "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ], - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,5e97ff834f5cd207162079ce925748a1" ] ], [ @@ -449,11 +331,8 @@ ], [ "test.deduped.sorted.MarkDuplicates.metrics.txt", - "test.sorted.bam", "test.flagstat", - "test.sorted.bam", "test.idxstats", - "test.sorted.bam", "test.stats" ], [ @@ -464,9 +343,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-30T16:07:51.260879823" + "timestamp": "2025-12-03T12:27:56.314782" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf index 8cb4cacdc..2ea496533 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf @@ -18,14 +18,13 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { use_gpu // boolean: whether to use GPU or CPU for bwameth alignment main: - - ch_alignment = Channel.empty() - ch_alignment_index = Channel.empty() - ch_samtools_flagstat = Channel.empty() - ch_samtools_stats = Channel.empty() - ch_picard_metrics = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_versions = Channel.empty() + ch_alignment = channel.empty() + ch_alignment_index = channel.empty() + ch_samtools_flagstat = channel.empty() + ch_samtools_stats = channel.empty() + ch_picard_metrics = channel.empty() + ch_multiqc_files = channel.empty() + ch_versions = channel.empty() /* * Align with bwameth @@ -64,7 +63,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { '' ) ch_alignment = SAMTOOLS_SORT.out.bam - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) /* * Run samtools index on alignment @@ -92,7 +90,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { [[:],[]] // [ [meta], [fasta]] ) ch_samtools_stats = SAMTOOLS_STATS.out.stats - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) if (!skip_deduplication) { /* @@ -119,17 +116,17 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { /* * Collect MultiQC inputs */ - ch_multiqc_files = ch_picard_metrics.collect{ meta, metrics -> metrics } - .mix(ch_samtools_flagstat.collect{ meta, flagstat -> flagstat }) - .mix(ch_samtools_stats.collect{ meta, stats -> stats }) + ch_multiqc_files = ch_picard_metrics.collect{ _meta, metrics -> metrics } + .mix(ch_samtools_flagstat.collect{ _meta, flagstat -> flagstat }) + .mix(ch_samtools_stats.collect{ _meta, stats -> stats }) emit: - bam = ch_alignment // channel: [ val(meta), [ bam ] ] - bai = ch_alignment_index // channel: [ val(meta), [ bai ] ] - samtools_flagstat = ch_samtools_flagstat // channel: [ val(meta), [ flagstat ] ] - samtools_stats = ch_samtools_stats // channel: [ val(meta), [ stats ] ] - picard_metrics = ch_picard_metrics // channel: [ val(meta), [ metrics ] ] - multiqc = ch_multiqc_files // channel: [ *{html,txt} ] - versions = ch_versions // channel: [ versions.yml ] + bam = ch_alignment // channel: [ val(meta), [ bam ] ] + bai = ch_alignment_index // channel: [ val(meta), [ bai ] ] + samtools_flagstat = ch_samtools_flagstat // channel: [ val(meta), [ flagstat ] ] + samtools_stats = ch_samtools_stats // channel: [ val(meta), [ stats ] ] + picard_metrics = ch_picard_metrics // channel: [ val(meta), [ metrics ] ] + multiqc = ch_multiqc_files // channel: [ *{html,txt} ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml index c85f88d35..338332e5a 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml @@ -84,9 +84,9 @@ output: - multiqc: type: file description: | - Channel containing MultiQC report aggregating results across samples. - Structure: [ val(meta), path(multiqc_report.html) ] - pattern: "*.html" + Channel containing files for MultiQC input (metrics, stats, flagstat). + Structure: [ path(files) ] + pattern: "*.{txt,stats,flagstat}" - versions: type: file description: | diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap index d4b27da21..021c089e3 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap @@ -34,11 +34,9 @@ "test.stats" ], [ - "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43", "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb", "versions.yml:md5,e9c5078a84e09a78756e7f9a5b1a9f89", "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" ] @@ -47,7 +45,7 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-13T16:57:26.654134509" + "timestamp": "2025-11-03T10:01:41.475172082" }, "Params: parabricks/fq2bammeth single-end | use_gpu | skip_deduplication": { "content": [ @@ -83,10 +81,8 @@ "test.stats" ], [ - "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43", "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb", "versions.yml:md5,e9c5078a84e09a78756e7f9a5b1a9f89" ] ], @@ -94,6 +90,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-13T16:58:18.600891908" + "timestamp": "2025-11-03T10:02:53.402903725" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test index 321d900f5..e64c44740 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test @@ -80,7 +80,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], + [ id:'test', single_end:false ], file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) ]) @@ -122,7 +122,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [ id:'test', single_end:true ], + [ id:'test', single_end:false ], file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) ]) diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap index 6ad8ba50c..885df4ab2 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap @@ -34,20 +34,18 @@ "test.stats" ], [ - "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43", "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", "versions.yml:md5,6c757564e855659911e8721c78ef6303", "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb", "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-16T19:27:14.082839334" + "timestamp": "2025-11-01T03:09:53.217361" }, "Params: bwameth paired-end | skip_deduplication": { "content": [ @@ -61,7 +59,7 @@ [ { "id": "test", - "single_end": true + "single_end": false }, "test.flagstat:md5,4ff87d121ca174953734723938c99081" ] @@ -70,7 +68,7 @@ [ { "id": "test", - "single_end": true + "single_end": false }, "test.stats:md5,8052e9c021ba6ebf5b7aed5538f7008f" ] @@ -83,18 +81,16 @@ "test.stats" ], [ - "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43", "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb" + "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-16T19:27:38.015666411" + "timestamp": "2025-12-03T12:40:33.660146" }, "Params: bwameth paired-end | default": { "content": [ @@ -108,7 +104,7 @@ [ { "id": "test", - "single_end": true + "single_end": false }, "test.flagstat:md5,4ff87d121ca174953734723938c99081" ] @@ -117,7 +113,7 @@ [ { "id": "test", - "single_end": true + "single_end": false }, "test.stats:md5,8052e9c021ba6ebf5b7aed5538f7008f" ] @@ -131,19 +127,17 @@ "test.stats" ], [ - "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43", "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", "versions.yml:md5,6c757564e855659911e8721c78ef6303", "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb", "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-16T19:27:27.812652475" + "timestamp": "2025-12-03T12:40:19.798072" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 2f30e9a46..bfd258760 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -98,7 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // diff --git a/tests/bismark_hisat_variants.nf.test.snap b/tests/bismark_hisat_variants.nf.test.snap index 64a61b619..765bad8ce 100644 --- a/tests/bismark_hisat_variants.nf.test.snap +++ b/tests/bismark_hisat_variants.nf.test.snap @@ -2,9 +2,6 @@ "Params: bismark_hisat with rrbs": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_GENOMEPREPARATION_HISAT": { "bismark": "0.25.1" }, @@ -17,18 +14,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -36,6 +27,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -51,14 +54,10 @@ "bismark_hisat/alignments/logs/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/alignments/logs/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/deduplicated", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark_hisat/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark_hisat/methylation_calls", "bismark_hisat/methylation_calls/bedGraph", "bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.bedGraph.gz", @@ -248,6 +247,7 @@ "multiqc/bismark_hisat/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -353,22 +353,6 @@ [ "SRR389222_sub3_trimmed_bismark_hisat2.bam", "9972d2444374fd93f4877867b786f1d2" - ], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "7f73f1e4398f697100a09d3742b662cb" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "926438a4e8a8fe56db5f99bd3b28ef0d" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "fdc1c2b1beb071e9b3dccb991f216ee0" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "99246979468cb998c02b26b5c8ac4ee4" ] ] ], @@ -376,14 +360,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T07:53:03.399744662" + "timestamp": "2025-12-04T10:32:32.15283" }, "Params: bismark_hisat with save_reference and save_align_intermeds": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -399,18 +380,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -418,18 +393,30 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ "bismark_hisat", "bismark_hisat/alignments", - "bismark_hisat/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bismark_hisat/alignments/Ecoli_10K_methylated.sorted.bam", "bismark_hisat/alignments/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.bam", - "bismark_hisat/alignments/SRR389222_sub1.deduplicated.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub1.sorted.bam", "bismark_hisat/alignments/SRR389222_sub1_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub2.deduplicated.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub2.sorted.bam", "bismark_hisat/alignments/SRR389222_sub2_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub3.deduplicated.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub3.sorted.bam", "bismark_hisat/alignments/SRR389222_sub3_trimmed_bismark_hisat2.bam", "bismark_hisat/alignments/logs", "bismark_hisat/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_PE_report.txt", @@ -437,14 +424,10 @@ "bismark_hisat/alignments/logs/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/alignments/logs/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/deduplicated", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark_hisat/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark_hisat/deduplicated/logs", "bismark_hisat/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.deduplication_report.txt", "bismark_hisat/deduplicated/logs/SRR389222_sub1_trimmed_bismark_hisat2.deduplication_report.txt", @@ -671,6 +654,7 @@ "multiqc/bismark_hisat/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -783,7 +767,7 @@ ], [ [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", + "Ecoli_10K_methylated.sorted.bam", "a1bd6455ebe3ecb43fe55e02d149d98" ], [ @@ -791,7 +775,7 @@ "534293d598c34366bcde057d3972b60" ], [ - "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.sorted.bam", "8d735d1f6337b2cf2fa720773ce34b60" ], [ @@ -799,7 +783,7 @@ "4ee84a71b73e58161226cc4d8ca1f9b9" ], [ - "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.sorted.bam", "45d53a598b4e59d173e32ea1f0558083" ], [ @@ -807,28 +791,12 @@ "3e3ccc351ed92abdced1edb24fbb94ed" ], [ - "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.sorted.bam", "ddb15c5ef0686837616d73f45c154b8d" ], [ "SRR389222_sub3_trimmed_bismark_hisat2.bam", "74c99f560772eb303bd4bc257f3a8898" - ], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a1bd6455ebe3ecb43fe55e02d149d98" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "8d735d1f6337b2cf2fa720773ce34b60" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "45d53a598b4e59d173e32ea1f0558083" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "ddb15c5ef0686837616d73f45c154b8d" ] ] ], @@ -836,14 +804,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T07:55:01.585305266" + "timestamp": "2025-12-04T10:35:05.513333" }, "Params: bismark_hisat": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -859,18 +824,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -878,6 +837,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -889,14 +860,10 @@ "bismark_hisat/alignments/logs/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/alignments/logs/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.txt", "bismark_hisat/deduplicated", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark_hisat/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark_hisat/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark_hisat/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark_hisat/deduplicated/logs", "bismark_hisat/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.deduplication_report.txt", "bismark_hisat/deduplicated/logs/SRR389222_sub1_trimmed_bismark_hisat2.deduplication_report.txt", @@ -1099,6 +1066,7 @@ "multiqc/bismark_hisat/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1191,28 +1159,13 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a1bd6455ebe3ecb43fe55e02d149d98" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "8d735d1f6337b2cf2fa720773ce34b60" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "45d53a598b4e59d173e32ea1f0558083" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "ddb15c5ef0686837616d73f45c154b8d" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T07:51:02.606421051" + "timestamp": "2025-12-04T10:29:59.500277" } } \ No newline at end of file diff --git a/tests/bismark_variants.nf.test.snap b/tests/bismark_variants.nf.test.snap index e71447096..9161026f3 100644 --- a/tests/bismark_variants.nf.test.snap +++ b/tests/bismark_variants.nf.test.snap @@ -2,9 +2,6 @@ "Params: bismark with run_qualimap": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -20,9 +17,6 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -32,9 +26,6 @@ "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -42,6 +33,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -53,14 +56,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -473,6 +472,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -534,7 +534,7 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,23036cfc6e2745e5a5bf67400b460bc1", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e06738420ad17564d41a789f2bdfd625", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,a4de33fbf4437c7714ab128067541043", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", + "genome_results.txt:md5,7886cc1a96ee892e49898b0d69ed66f2", "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4", "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e", "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25", @@ -546,7 +546,7 @@ "mapped_reads_nucleotide_content.txt:md5,2e1916f7c31072e65529c44069be69bd", "mapping_quality_across_reference.txt:md5,7b29de82fbdad93249121e694f09abb2", "mapping_quality_histogram.txt:md5,9dc98cc4e42f82a21f438c349e7e55db", - "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", + "genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15", "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803", "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2", "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1", @@ -555,7 +555,7 @@ "mapped_reads_nucleotide_content.txt:md5,2a2d04e030d228b9e6c3267e6f9e6225", "mapping_quality_across_reference.txt:md5,33942e63dd23b4c0e307cd2f8c2fb299", "mapping_quality_histogram.txt:md5,5d14a661b9d3d59e4dfcb841084a6def", - "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", + "genome_results.txt:md5,7838069da6060f756821c776cc3a4929", "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2", "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80", "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8", @@ -564,7 +564,7 @@ "mapped_reads_nucleotide_content.txt:md5,ffdced213cd2a96408c4b9794092bd80", "mapping_quality_across_reference.txt:md5,a15709e1860fdd7deaf86dfa0d461144", "mapping_quality_histogram.txt:md5,feafb188d85e486d16374117565d88d1", - "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a", + "genome_results.txt:md5,41aa314da188306ead441ddcb14f79b2", "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce", "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301", "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b", @@ -609,36 +609,18 @@ "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:17:45.757115349" + "timestamp": "2025-12-04T09:46:07.81674" }, "Params: bismark with nomeseq": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_COVERAGE2CYTOSINE": { "bismark": "0.25.1" }, @@ -657,18 +639,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -676,6 +652,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -711,14 +699,10 @@ "bismark/coverage2cytosine/summaries/SRR389222_sub2.cytosine_context_summary.txt", "bismark/coverage2cytosine/summaries/SRR389222_sub3.cytosine_context_summary.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -921,6 +905,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1033,36 +1018,18 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:11:00.32448738" + "timestamp": "2025-12-04T09:39:52.12429" }, "Params: bismark with skip_multiqc": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -1078,18 +1045,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1097,6 +1058,15 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -1108,14 +1078,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -1189,6 +1155,7 @@ "fastqc/zips/SRR389222_sub3_fastqc.zip", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1252,36 +1219,18 @@ "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,a4de33fbf4437c7714ab128067541043" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:19:27.705338625" + "timestamp": "2025-12-04T10:21:20.309779" }, "Params: bismark (default)": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -1297,18 +1246,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1316,6 +1259,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -1327,14 +1282,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -1537,6 +1488,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1629,36 +1581,18 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T07:59:11.539725915" + "timestamp": "2025-12-04T09:24:24.47393" }, "Params: bismark with cytosine_report": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_COVERAGE2CYTOSINE": { "bismark": "0.25.1" }, @@ -1677,18 +1611,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1696,6 +1624,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -1719,14 +1659,10 @@ "bismark/coverage2cytosine/summaries/SRR389222_sub2.cytosine_context_summary.txt", "bismark/coverage2cytosine/summaries/SRR389222_sub3.cytosine_context_summary.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -1929,6 +1865,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -2029,36 +1966,18 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:04:57.827583264" + "timestamp": "2025-12-04T09:31:52.676835" }, "Params: bismark with em_seq and clip_r1": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -2074,18 +1993,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -2093,6 +2006,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -2104,14 +2029,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - 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[ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "8c57faf8f2ea0619982046c6aa92d518" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "1b2b7cfc2ac6ff065b4708b4e2b997f" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "685a11fcb763614e081c4a82f2d63844" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "9c08b7ac915ada7fefb8435460ccb651" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:08:53.462561913" + "timestamp": "2025-12-04T09:36:55.032483" }, "Params: bismark with skip_trimming": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -2451,20 +2355,26 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -2476,14 +2386,10 @@ "bismark/alignments/logs/SRR389222_sub2_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_bismark_bt2_SE_report.txt", "bismark/deduplicated", - 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}, "BISMARK_GENOMEPREPARATION_BOWTIE": { "bismark": "0.25.1" }, @@ -2781,18 +2670,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -2800,6 +2683,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -2822,7 +2717,6 @@ "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", - "bismark/deduplicated", "bismark/methylation_calls", "bismark/methylation_calls/bedGraph", "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bedGraph.gz", @@ -3012,6 +2906,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -3140,14 +3035,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - 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], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "38e388c7f8db48f3e06d16d2611faafe" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "d042804716ccaa1f8061a309e8d79467" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "a55f63182990117bc57714cb8227a57e" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "605fc4a383cc488c53b66c6b5494eba" ] ] ], @@ -3519,14 +3398,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:06:59.451400542" + "timestamp": "2025-12-04T09:34:27.286737" }, "Params: bismark with save_reference and save_align_intermeds": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -3542,18 +3418,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -3561,18 +3431,30 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ "bismark", "bismark/alignments", - "bismark/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam", "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", - "bismark/alignments/SRR389222_sub1.deduplicated.sorted.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam", "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub2.deduplicated.sorted.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam", "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub3.deduplicated.sorted.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam", "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", @@ -3580,14 +3462,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -3810,6 +3688,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -3918,7 +3797,7 @@ ], [ [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", + "Ecoli_10K_methylated.sorted.bam", "a54ab7c96f9523a4ccd25fd69f6905f8" ], [ @@ -3926,7 +3805,7 @@ "fad4414ebdaafdb15e0584b393400b27" ], [ - "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.sorted.bam", "3f11ef5fbbda3797fd6217728e4f00d3" ], [ @@ -3934,7 +3813,7 @@ "934288bfc59d40ff7e73706d07815fb" ], [ - "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.sorted.bam", "b01f29fc1d8d46922a69df09c636b4c4" ], [ @@ -3942,28 +3821,12 @@ "a94aeadc2acebd0a46647bb95acf2d55" ], [ - "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.sorted.bam", "347195c04c9ffd2a2b10967a6682fc69" ], [ "SRR389222_sub3_trimmed_bismark_bt2.bam", "6579ca7e49b9d7760ea5b3f3456739a1" - ], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" ] ] ], @@ -3971,14 +3834,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:12:58.138668044" + "timestamp": "2025-12-04T09:42:24.400932" }, "Params: bismark with CAT_FASTQ and skip_trimming and skip_deduplication": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_GENOMEPREPARATION_BOWTIE": { "bismark": "0.25.1" }, @@ -3994,20 +3854,26 @@ "CAT_FASTQ": { "cat": 9.5 }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -4022,7 +3888,6 @@ "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt", "bismark/alignments/logs/SRR389222.merged_bismark_bt2_SE_report.txt", - "bismark/deduplicated", "bismark/methylation_calls", "bismark/methylation_calls/bedGraph", "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz", @@ -4171,7 +4036,8 @@ "multiqc/bismark/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_methylseq_software_mqc_versions.yml" + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml" ], [ "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", @@ -4242,14 +4108,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:22:52.58616656" + "timestamp": "2025-12-04T10:25:14.441173" }, "Params: bismark with run_preseq": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -4265,18 +4128,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -4284,6 +4141,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -4295,14 +4164,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -4505,6 +4370,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -4597,36 +4463,18 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:14:56.553076652" + "timestamp": "2025-12-04T10:16:18.019771" }, "Params: bismark with skip_fastqc": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -4648,9 +4496,6 @@ "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -4658,6 +4503,15 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -4669,14 +4523,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -4822,6 +4672,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -4903,28 +4754,13 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:21:14.550967256" + "timestamp": "2025-12-04T10:23:38.468009" } } \ No newline at end of file diff --git a/tests/bwamem_taps.nf.test.snap b/tests/bwamem_taps.nf.test.snap index c98b3a037..ae8490785 100644 --- a/tests/bwamem_taps.nf.test.snap +++ b/tests/bwamem_taps.nf.test.snap @@ -9,9 +9,6 @@ "bwa": "0.7.19-r1273", "samtools": "1.22.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -34,14 +31,22 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ "bwa", - "bwa/Ecoli_10K_methylated.bam", - "bwa/SRR389222_sub1.bam", - "bwa/SRR389222_sub2.bam", - "bwa/SRR389222_sub3.bam", "bwa/bwa", "bwa/bwa/genome.amb", "bwa/bwa/genome.ann", @@ -60,22 +65,18 @@ "bwamem/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwamem/alignments/samtools_stats/SRR389222_sub3.stats", "bwamem/deduplicated", - "bwamem/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bwamem/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", "bwamem/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwamem/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwamem/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bwamem/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", + "bwamem/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", "bwamem/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwamem/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwamem/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bwamem/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub1.sorted.bam.bai", "bwamem/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwamem/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwamem/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bwamem/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub2.sorted.bam.bai", "bwamem/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwamem/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", + "bwamem/deduplicated/SRR389222_sub3.sorted.bam.bai", "bwamem/deduplicated/picard_metrics", "bwamem/deduplicated/picard_metrics/Ecoli_10K_methylated.markdup.sorted.MarkDuplicates.metrics.txt", "bwamem/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -231,6 +232,7 @@ "picard/SRR389222_sub3.bam", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "rastair", "rastair/call", "rastair/call/Ecoli_10K_methylated.rastair_call.txt", @@ -278,23 +280,19 @@ "trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt" ], [ - "Ecoli_10K_methylated.bam:md5,2f4f23ea06de8e6bd8dee078b0d60959", - "SRR389222_sub1.bam:md5,92bb30934b2f0c89d41b305208deacaa", - "SRR389222_sub2.bam:md5,692f79036f925dc4b8e3056de1f5a6df", - "SRR389222_sub3.bam:md5,a40e01491a69629afdf7c82d4a430a27", "genome.amb:md5,c5a18088a0c677c9cdcebec36f2cf418", "genome.ann:md5,78b2fd32c283fbf8ba7624b883349a57", "genome.bwt:md5,86b95928f5c901663ce25d41631a97db", "genome.pac:md5,27c59f7f0708bb35ad99f502c2b33ab7", "genome.sa:md5,85d7f8991619c22bd892471e036b8069", "Ecoli_10K_methylated.flagstat:md5,6875b2d49eec4f8b199bceda4f3ab148", - "Ecoli_10K_methylated.stats:md5,461532b534657aac1cb6b099dd4eaa8d", + "Ecoli_10K_methylated.stats:md5,d0cdfe71937342f869ad66a55b3ef369", "SRR389222_sub1.flagstat:md5,fbfec3e5592cbb11f050ed06983f2bbd", - "SRR389222_sub1.stats:md5,6eada49b29ebb02dbb9c4858fb95608a", + "SRR389222_sub1.stats:md5,f498a01fafd4a576a787ac846a5a4730", "SRR389222_sub2.flagstat:md5,0ad57bb4ef7b258fc23d9b3ab7ed26b4", - "SRR389222_sub2.stats:md5,ed79887eadefeb3cebe35b1bf1f7155c", + "SRR389222_sub2.stats:md5,3d6efc44145295bbfd793e89f6e46acd", "SRR389222_sub3.flagstat:md5,c6e3f93f66e47ff2138f640eaebd1c3b", - "SRR389222_sub3.stats:md5,b7590442506673c27e85595d3aa75ef7", + "SRR389222_sub3.stats:md5,e109c00d56f1cf2866106cccc45706b9", "cutadapt_filtered_reads_plot.txt:md5,ff1b6d4011a5be5410b9404f7ff56c56", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,57d07c19b0c30dc88df96c30bedcdc33", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,1e5ca4193f8290c5c812334d03615b41", @@ -327,10 +325,10 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,474c4c51b3f330261d1b8a9c9995e4d8", "samtools-stats-dp.txt:md5,ee0270689f78b57905ebd812bb87891b", "samtools_alignment_plot.txt:md5,3a748a90ccfbb3e55811b71bcb1eece8", - "Ecoli_10K_methylated.bam:md5,fd51cc77bf6d05801f6e1a80eb0abf25", - "SRR389222_sub1.bam:md5,1af31feb044c3364e69fdfa93f8b8e2d", - "SRR389222_sub2.bam:md5,88c1e75afa1f068f2cd5a0ff550b713e", - "SRR389222_sub3.bam:md5,5ad6e81a73fb06c47eef074902ddf147", + "Ecoli_10K_methylated.bam:md5,180c690adcffe119a059ef4016932b92", + "SRR389222_sub1.bam:md5,283d34099977aebacd1e4fe8e24ab0ab", + "SRR389222_sub2.bam:md5,e521543564ffb76300c6f5b82a037b2d", + "SRR389222_sub3.bam:md5,fd2e341084f4abed03cecae4bef80a82", "Ecoli_10K_methylated.rastair_call.txt:md5,23f789a8fe5a457e368f36e02a87ecb2", "SRR389222_sub1.rastair_call.txt:md5,23f789a8fe5a457e368f36e02a87ecb2", "SRR389222_sub2.rastair_call.txt:md5,23f789a8fe5a457e368f36e02a87ecb2", @@ -353,50 +351,18 @@ "SRR389222_sub3.idxstats:md5,59fa8ca802e25072377a7527a6801f9b" ], [ - [ - "Ecoli_10K_methylated.bam", - "ab11b56e62ca10400198aeaf7ff734e3" - ], - [ - "SRR389222_sub1.bam", - "afd6b0434556e362a677a5f6bf75e214" - ], - [ - "SRR389222_sub2.bam", - "13bf6e409b464c7ef60dc8d2757daa9c" - ], - [ - "SRR389222_sub3.bam", - "7934578fa655119e9ab995fe8e793f44" - ], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "ab11b56e62ca10400198aeaf7ff734e3" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "ab11b56e62ca10400198aeaf7ff734e3" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "afd6b0434556e362a677a5f6bf75e214" - ], [ "SRR389222_sub1.markdup.sorted.bam", "afd6b0434556e362a677a5f6bf75e214" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "13bf6e409b464c7ef60dc8d2757daa9c" - ], [ "SRR389222_sub2.markdup.sorted.bam", "13bf6e409b464c7ef60dc8d2757daa9c" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "7934578fa655119e9ab995fe8e793f44" - ], [ "SRR389222_sub3.markdup.sorted.bam", "7934578fa655119e9ab995fe8e793f44" @@ -423,6 +389,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:26:33.748739744" + "timestamp": "2025-12-04T10:39:11.815644" } } \ No newline at end of file diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap index 20ed8efa2..38ea9d653 100644 --- a/tests/bwameth_use_gpu.nf.test.snap +++ b/tests/bwameth_use_gpu.nf.test.snap @@ -5,9 +5,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -32,12 +29,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -45,6 +36,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -58,13 +61,10 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -187,6 +187,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/SRR389222_sub1_trimmed_fastqc.html", @@ -203,11 +204,11 @@ ], [ "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", "SRR389222_sub3.markdup.sorted_CpG.bedGraph:md5,a91e6b039e9581a9d2ef6f6057918b39", @@ -241,26 +242,14 @@ "samtools_alignment_plot.txt:md5,34b8fa8a88b6f5ef00153b07aabc028d" ], [ - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "97e6767c5ddea54cb2a6498192a09c68" - ], [ "SRR389222_sub1.markdup.sorted.bam", "97e6767c5ddea54cb2a6498192a09c68" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "313ae71af4023059a295ed8a132fd9ad" - ], [ "SRR389222_sub2.markdup.sorted.bam", "313ae71af4023059a295ed8a132fd9ad" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "9eaa07df5ad58a78ab57ee55f948a044" - ], [ "SRR389222_sub3.markdup.sorted.bam", "9eaa07df5ad58a78ab57ee55f948a044" @@ -269,8 +258,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T22:06:32.281942361" + "timestamp": "2025-12-06T18:29:01.898537657" } } \ No newline at end of file diff --git a/tests/bwameth_variants.nf.test.snap b/tests/bwameth_variants.nf.test.snap index cfc5ba73c..76a58042c 100644 --- a/tests/bwameth_variants.nf.test.snap +++ b/tests/bwameth_variants.nf.test.snap @@ -8,9 +8,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -35,12 +32,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -48,6 +39,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -63,16 +66,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -372,6 +371,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -394,13 +394,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", "coverage_across_reference.txt:md5,c4c7f930ad577d15de1358226acab252", "coverage_histogram.txt:md5,cddf42d662856425649c196c731f048b", @@ -460,34 +460,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -498,7 +482,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:37:31.53335091" + "timestamp": "2025-12-04T10:49:57.004367" }, "Params: bwameth with skip_deduplication": { "content": [ @@ -509,9 +493,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -527,12 +508,6 @@ "SAMTOOLS_INDEX_ALIGNMENTS": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -540,6 +515,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -558,7 +545,6 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", - "bwameth/deduplicated", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -681,6 +667,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -764,7 +751,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:32:43.517125394" + "timestamp": "2025-12-04T10:45:40.098015" }, "Params: bwameth with skip_fastqc": { "content": [ @@ -796,12 +783,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -809,6 +790,15 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -824,16 +814,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -918,6 +904,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -940,13 +927,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -974,34 +961,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -1012,7 +983,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:38:50.632236108" + "timestamp": "2025-12-04T10:51:08.552779" }, "Params: bwameth with CAT_FASTQ and skip_trimming and skip_deduplication": { "content": [ @@ -1026,9 +997,6 @@ "CAT_FASTQ": { "cat": 9.5 }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1044,14 +1012,20 @@ "SAMTOOLS_INDEX_ALIGNMENTS": { "samtools": "1.22.1" }, + "Workflow": { + "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_STATS": { "samtools": "1.22.1" - }, - "Workflow": { - "nf-core/methylseq": "v4.2.0dev" } }, [ @@ -1064,7 +1038,6 @@ "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", "bwameth/alignments/samtools_stats/SRR389222.flagstat", "bwameth/alignments/samtools_stats/SRR389222.stats", - "bwameth/deduplicated", "cat", "cat/SRR389222.merged.fastq.gz", "fastqc", @@ -1164,7 +1137,8 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_methylseq_software_mqc_versions.yml" + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml" ], [ "Ecoli_10K_methylated.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", @@ -1210,7 +1184,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:41:07.419799556" + "timestamp": "2025-12-04T10:53:10.63052" }, "Params: bwameth": { "content": [ @@ -1221,9 +1195,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1245,12 +1216,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1258,6 +1223,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -1273,16 +1250,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -1424,6 +1397,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1446,13 +1420,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1491,34 +1465,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -1529,7 +1487,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:28:29.73934595" + "timestamp": "2025-12-04T10:41:44.414841" }, "Params: bwameth with skip_multiqc": { "content": [ @@ -1540,9 +1498,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1564,12 +1519,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1577,6 +1526,15 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -1592,16 +1550,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -1633,6 +1587,7 @@ "methyldackel/mbias/SRR389222_sub3.mbias.txt", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1655,13 +1610,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1672,34 +1627,18 @@ "SRR389222_sub3.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -1710,7 +1649,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:40:12.19993791" + "timestamp": "2025-12-04T10:52:27.013821" }, "Params: bwameth with skip_trimming": { "content": [ @@ -1721,9 +1660,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1745,14 +1681,20 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, + "Workflow": { + "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_STATS": { "samtools": "1.22.1" - }, - "Workflow": { - "nf-core/methylseq": "v4.2.0dev" } }, [ @@ -1768,16 +1710,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -1902,17 +1840,18 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_methylseq_software_mqc_versions.yml" + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml" ], [ "Ecoli_10K_methylated.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", - "Ecoli_10K_methylated.stats:md5,0bc7e32cf2a553fad5d5411fdaf28e37", + "Ecoli_10K_methylated.stats:md5,0b2637c18e999db79658704acaba7487", "SRR389222_sub1.flagstat:md5,897d500a710a56a7098172167fa71108", - "SRR389222_sub1.stats:md5,d567d8d2d8af5f11ccc78c03003dba0a", + "SRR389222_sub1.stats:md5,96ff5c683aed6e243cf451994e47e88d", "SRR389222_sub2.flagstat:md5,37d33d68b31d4550620dc17582a3a750", - "SRR389222_sub2.stats:md5,9d03aaab50012328c6d4a7a5455565d9", + "SRR389222_sub2.stats:md5,8ab151baed3d6787d212e65c819bd51f", "SRR389222_sub3.flagstat:md5,e3e925a7b7356e93d14f5e9e102c55b7", - "SRR389222_sub3.stats:md5,8a5bbb8b04df08d8d68153516cb41710", + "SRR389222_sub3.stats:md5,cd1b0557ab452a7672c89790caf43e0d", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,b43c4c8ff346ae865b2b5db996650942", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -1947,34 +1886,18 @@ "samtools_alignment_plot.txt:md5,fe4c9af19d69c3982b75ad458a1a9148" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "5b485bcabdb1ad5955cfa061741fad31" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "5b485bcabdb1ad5955cfa061741fad31" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "37ec1c6338cc3fee7ab1cb2d48dba38" - ], [ "SRR389222_sub1.markdup.sorted.bam", "37ec1c6338cc3fee7ab1cb2d48dba38" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "783d3be6b5bfa58142c3dbe864f6d8c5" - ], [ "SRR389222_sub2.markdup.sorted.bam", "783d3be6b5bfa58142c3dbe864f6d8c5" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "4bbaef9917f4ff0248d1f5853f583fd0" - ], [ "SRR389222_sub3.markdup.sorted.bam", "4bbaef9917f4ff0248d1f5853f583fd0" @@ -1985,7 +1908,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:31:30.099089438" + "timestamp": "2025-12-04T10:44:28.215245" }, "Params: bwameth with mem2 index": { "content": [ @@ -1996,9 +1919,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -2020,12 +1940,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -2033,6 +1947,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -2048,16 +1974,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -2199,6 +2121,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -2221,13 +2144,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -2266,34 +2189,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -2304,7 +2211,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:30:05.831910961" + "timestamp": "2025-12-04T10:43:13.595208" }, "Params: bwameth with save_reference and save_align_intermeds": { "content": [ @@ -2315,9 +2222,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -2339,12 +2243,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -2352,23 +2250,35 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ "bwameth", "bwameth/alignments", "bwameth/alignments/Ecoli_10K_methylated.bam", - "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub1.bam", - "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam", - "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub1.sorted.bam", + "bwameth/alignments/SRR389222_sub1.sorted.bam.bai", "bwameth/alignments/SRR389222_sub2.bam", - "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam", - "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub2.sorted.bam", + "bwameth/alignments/SRR389222_sub2.sorted.bam.bai", "bwameth/alignments/SRR389222_sub3.bam", - "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam", - "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub3.sorted.bam", + "bwameth/alignments/SRR389222_sub3.sorted.bam.bai", "bwameth/alignments/samtools_stats", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", @@ -2379,16 +2289,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -2538,6 +2444,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -2560,13 +2467,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", @@ -2616,7 +2523,7 @@ "4a9ba2169facef4ed3d92d539c8c78af" ], [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", + "Ecoli_10K_methylated.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], [ @@ -2624,7 +2531,7 @@ "e50275d6d44138f19d65ee479444d5ce" ], [ - "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], [ @@ -2632,7 +2539,7 @@ "d365b8b2662b2abffb51dd67a1f463b4" ], [ - "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], [ @@ -2640,37 +2547,21 @@ "a9fd2900b9d759f8f4f62cbbb2744fde" ], [ - "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" ], - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -2681,7 +2572,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:35:42.305102421" + "timestamp": "2025-12-04T10:48:17.999837" }, "Params: bwameth with rrbs": { "content": [ @@ -2692,9 +2583,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -2710,12 +2598,6 @@ "SAMTOOLS_INDEX_ALIGNMENTS": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -2723,6 +2605,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -2737,11 +2631,6 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", - "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -2755,10 +2644,10 @@ "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", "methyldackel", - "methyldackel/Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub1.deduplicated.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub2.deduplicated.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub3.deduplicated.sorted_CpG.bedGraph", + "methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub1.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub2.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub3.sorted_CpG.bedGraph", "methyldackel/mbias", "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", "methyldackel/mbias/SRR389222_sub1.mbias.txt", @@ -2864,6 +2753,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -2886,17 +2776,17 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,c6a9a8b50c5e1d239071a8b75bc63b4f", - "Ecoli_10K_methylated.stats:md5,0d3e87dd75fc1c6bce803874a1258ce3", + "Ecoli_10K_methylated.stats:md5,7a11b7c746dd231a3879545ba72478e0", "SRR389222_sub1.flagstat:md5,cccae088e2f8686b890d019b60f63065", - "SRR389222_sub1.stats:md5,e0105b286be3c3670f7da0c597610c50", + "SRR389222_sub1.stats:md5,71a786ffb2d4997c46512e06397d619a", "SRR389222_sub2.flagstat:md5,403af1bed1e3e96f5e04d65e96728828", - "SRR389222_sub2.stats:md5,f3ab2b63007d4377d3d19861bebb295d", + "SRR389222_sub2.stats:md5,9b018290dcd1525f5de1d17549beccfe", "SRR389222_sub3.flagstat:md5,73a5cb246f6388d5d449775d6e35f5fa", - "SRR389222_sub3.stats:md5,2326212674079f8455f2972c75603445", - "Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph:md5,aa55074c144aa6eaa184480038c75932", - "SRR389222_sub1.deduplicated.sorted_CpG.bedGraph:md5,9e9e6922a8d99881874d299bfd7af5de", - "SRR389222_sub2.deduplicated.sorted_CpG.bedGraph:md5,d6c973d9fa7c6bc5f47141d14c18a105", - "SRR389222_sub3.deduplicated.sorted_CpG.bedGraph:md5,0ce36f42cc865eb59c7c6fd43d016d2c", + "SRR389222_sub3.stats:md5,5fce6a66ddfb494e56755f6dd517d9e9", + "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,5e0bf8c8bb3162de75203784414a6399", + "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", + "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", + "SRR389222_sub3.sorted_CpG.bedGraph:md5,70dcc3836dc9721c2de367d1cf05e815", "Ecoli_10K_methylated.mbias.txt:md5,7fb217502c2f3ae955bdfd744b6cbb72", "SRR389222_sub1.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", "SRR389222_sub2.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", @@ -2925,28 +2815,13 @@ "samtools_alignment_plot.txt:md5,e10b792693e5a69776f623f5f7de647e" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "8039fd2db60f8ca71daa444e62411f53" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "a75ccc7cde779aac54662b03e5c01fe0" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "82d2a7df2d4cb1ed2ea1e0456aff1cb" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "7856b5549c566fb795c46f0674e069e1" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:34:02.797104294" + "timestamp": "2025-12-04T10:46:50.604131" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b66fa1811..c7fc9409a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -2,9 +2,6 @@ "-profile test": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -20,18 +17,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -39,6 +30,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -50,14 +53,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -260,6 +259,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -352,28 +352,13 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T08:43:18.101372902" + "timestamp": "2025-12-04T10:56:51.276142" } } \ No newline at end of file diff --git a/tests/index_downloads.nf.test.snap b/tests/index_downloads.nf.test.snap index ae91a7563..3923d56a0 100644 --- a/tests/index_downloads.nf.test.snap +++ b/tests/index_downloads.nf.test.snap @@ -2,9 +2,6 @@ "Params: default with bowtie2-index": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -17,28 +14,34 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, "pigz": 2.8 }, - "UNTAR": { + "UNTAR_BISMARK": { "untar": 1.34 }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } } ], @@ -46,14 +49,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T05:40:58.820369822" + "timestamp": "2025-12-04T11:02:11.64102" }, "Params: bismark_hisat with hisat2-index": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -69,18 +69,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -88,6 +82,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } } ], @@ -95,14 +101,11 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T05:46:24.84862466" + "timestamp": "2025-12-04T11:08:29.489122" }, "Params: bismark with run_preseq with bowtie2-index": { "content": [ { - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -115,28 +118,34 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, "pigz": 2.8 }, - "UNTAR": { + "UNTAR_BISMARK": { "untar": 1.34 }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } } ], @@ -144,7 +153,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T05:42:55.658790031" + "timestamp": "2025-12-04T11:04:35.596818" }, "Params: bwameth with bwameth-index": { "content": [ @@ -152,9 +161,6 @@ "BWAMETH_ALIGN": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -176,22 +182,28 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, "pigz": 2.8 }, - "UNTAR": { + "UNTAR_BWAMETH": { "untar": 1.34 }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } } ], @@ -199,6 +211,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T05:44:29.266621491" + "timestamp": "2025-12-04T11:06:00.333714" } } \ No newline at end of file diff --git a/tests/targeted_sequencing_variants.nf.test.snap b/tests/targeted_sequencing_variants.nf.test.snap index 43cc3fd38..ce705b349 100644 --- a/tests/targeted_sequencing_variants.nf.test.snap +++ b/tests/targeted_sequencing_variants.nf.test.snap @@ -11,9 +11,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -35,12 +32,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -48,6 +39,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -63,16 +66,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -218,6 +217,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -240,13 +240,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "Ecoli_10K_methylated.markdup.sorted_CpG.targeted.bedGraph:md5,1f3b38af3cf3c2cdf82fe38bb06ae547", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", @@ -289,34 +289,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -327,7 +311,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-28T13:46:29.932282" + "timestamp": "2025-12-04T11:12:45.73014" }, "Params: bismark with run_targeted_sequencing and collecthsmetrics": { "content": [ @@ -335,9 +319,6 @@ "BEDTOOLS_INTERSECT": { "bedtools": "2.31.1" }, - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -353,9 +334,6 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -368,9 +346,6 @@ "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -378,6 +353,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -389,14 +376,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -605,6 +588,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -701,29 +685,14 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-28T13:51:52.004183" + "timestamp": "2025-12-04T11:18:18.902199" }, "Params: bismark with run_targeted_sequencing": { "content": [ @@ -731,9 +700,6 @@ "BEDTOOLS_INTERSECT": { "bedtools": "2.31.1" }, - "BISMARK_ALIGN": { - "bismark": "0.25.1" - }, "BISMARK_DEDUPLICATE": { "bismark": "0.25.1" }, @@ -749,18 +715,12 @@ "BISMARK_SUMMARY": { "bismark": "0.25.1" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, "SAMTOOLS_INDEX": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -768,6 +728,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "BISMARK_ALIGN": { + "bismark": "0.25.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" } }, [ @@ -779,14 +751,10 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.sorted.bam.bai", "bismark/deduplicated/logs", "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", @@ -993,6 +961,7 @@ "multiqc/bismark/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1089,29 +1058,14 @@ "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" - ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "3f11ef5fbbda3797fd6217728e4f00d3" - ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "b01f29fc1d8d46922a69df09c636b4c4" - ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "347195c04c9ffd2a2b10967a6682fc69" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-28T13:45:07.649845" + "timestamp": "2025-12-04T11:11:18.208427" }, "Params: bwameth with run_targeted_sequencing and collecthsmetrics": { "content": [ @@ -1125,9 +1079,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1155,12 +1106,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1168,6 +1113,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -1183,16 +1140,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -1340,6 +1293,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1362,13 +1316,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "Ecoli_10K_methylated.markdup.sorted_CpG.targeted.bedGraph:md5,1f3b38af3cf3c2cdf82fe38bb06ae547", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", @@ -1411,34 +1365,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -1449,7 +1387,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-28T13:49:22.675999" + "timestamp": "2025-12-04T11:15:47.279014" }, "Params: bwameth with all_contexts and run_targeted_sequencing": { "content": [ @@ -1463,9 +1401,6 @@ "BWAMETH_INDEX": { "bwameth": "0.2.9" }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GUNZIP": { "gunzip": 1.13 }, @@ -1487,12 +1422,6 @@ "SAMTOOLS_INDEX_DEDUPLICATED": { "samtools": "1.22.1" }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "TRIMGALORE": { "trimgalore": "0.6.10", "cutadapt": 4.9, @@ -1500,6 +1429,18 @@ }, "Workflow": { "nf-core/methylseq": "v4.2.0dev" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "MULTIQC": { + "multiqc": 1.32 + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" } }, [ @@ -1515,16 +1456,12 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", - "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", - "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -1686,6 +1623,7 @@ "multiqc/bwameth/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", + "pipeline_info/nf_core_methylseq_topic_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -1708,13 +1646,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,72378a080b60e5ab2b78a64a92519c46", + "Ecoli_10K_methylated.stats:md5,4dd1be7514d159967c5b91866a980655", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,4013e8ea34581832fd7335d472efd369", + "SRR389222_sub1.stats:md5,638e03d7a02d8e7ce8694aab73f1e163", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,2991fbed406e6f76448d3e033484bdb2", + "SRR389222_sub2.stats:md5,43352aa3930321f587adf80b38d25cef", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,4dc3067cc6f490ec1ff28d1b00475375", + "SRR389222_sub3.stats:md5,470b6040d2b5832bd34989837c47a3e6", "Ecoli_10K_methylated.markdup.sorted_CHG.bedGraph:md5,9ae25ac4e62f8945e666a41bfc73f085", "Ecoli_10K_methylated.markdup.sorted_CHG.targeted.bedGraph:md5,1c9bd5a4d4c52f82a2a3d5e28bbde7ab", "Ecoli_10K_methylated.markdup.sorted_CHH.bedGraph:md5,1048980ecaaf99cba98f66fcf65cee94", @@ -1773,34 +1711,18 @@ "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a2921f761f431ede522016f83f75c12d" - ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], - [ - "SRR389222_sub1.deduplicated.sorted.bam", - "e50275d6d44138f19d65ee479444d5ce" - ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], - [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d365b8b2662b2abffb51dd67a1f463b4" - ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], - [ - "SRR389222_sub3.deduplicated.sorted.bam", - "a9fd2900b9d759f8f4f62cbbb2744fde" - ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -1811,6 +1733,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-28T13:47:53.001822" + "timestamp": "2025-12-04T11:14:14.394458" } } \ No newline at end of file diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 0216d0dcb..9630375df 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -4,26 +4,26 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryMap } from 'plugin/nf-schema' -include { FASTQC } from '../../modules/nf-core/fastqc/main' -include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' -include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' -include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' -include { MULTIQC } from '../../modules/nf-core/multiqc/main' -include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' -include { FASTQ_ALIGN_DEDUP_BISMARK } from '../../subworkflows/nf-core/fastq_align_dedup_bismark/main' -include { FASTQ_ALIGN_DEDUP_BWAMETH } from '../../subworkflows/nf-core/fastq_align_dedup_bwameth/main' -include { FASTQ_ALIGN_DEDUP_BWAMEM } from '../../subworkflows/nf-core/fastq_align_dedup_bwamem/main' -include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { FASTQC } from '../../modules/nf-core/fastqc/main' +include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' +include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' +include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' +include { FASTQ_ALIGN_DEDUP_BISMARK } from '../../subworkflows/nf-core/fastq_align_dedup_bismark/main' +include { FASTQ_ALIGN_DEDUP_BWAMETH } from '../../subworkflows/nf-core/fastq_align_dedup_bwameth/main' +include { FASTQ_ALIGN_DEDUP_BWAMEM } from '../../subworkflows/nf-core/fastq_align_dedup_bwamem/main' +include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' include { PICARD_ADDORREPLACEREADGROUPS } from '../../modules/nf-core/picard/addorreplacereadgroups/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { BAM_TAPS_CONVERSION } from '../../subworkflows/nf-core/bam_taps_conversion' -include { BAM_METHYLDACKEL } from '../../subworkflows/nf-core/bam_methyldackel/main' -include { TARGETED_SEQUENCING } from '../../subworkflows/local/targeted_sequencing' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { BAM_TAPS_CONVERSION } from '../../subworkflows/nf-core/bam_taps_conversion' +include { BAM_METHYLDACKEL } from '../../subworkflows/nf-core/bam_methyldackel/main' +include { TARGETED_SEQUENCING } from '../../subworkflows/local/targeted_sequencing' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52,6 +52,10 @@ workflow METHYLSEQ { ch_gzi = channel.empty() ch_bedgraph = channel.empty() ch_aligner_mqc = channel.empty() + ch_rastair_mbias = channel.empty() + ch_rastair_call = channel.empty() + ch_methylkit = channel.empty() + ch_mbias = channel.empty() ch_qualimap = channel.empty() ch_preseq = channel.empty() ch_multiqc_files = channel.empty() @@ -85,7 +89,6 @@ workflow METHYLSEQ { ) ch_fastqc_html = FASTQC.out.html ch_fastqc_zip = FASTQC.out.zip - ch_versions = ch_versions.mix(FASTQC.out.versions) } else { ch_fastqc_html = channel.empty() ch_fastqc_zip = channel.empty() @@ -108,9 +111,8 @@ workflow METHYLSEQ { // SUBWORKFLOW: Align reads, deduplicate and extract methylation with Bismark // - if (params.taps & params.aligner != 'bwamem') { + if (params.taps && params.aligner != 'bwamem') { log.info "TAPS protocol detected and aligner is not 'bwamem'. We recommend using bwa-mem for TAPS protocol as it is optimized for this type of data." - // params.aligner = 'bwamem' } // Aligner: bismark or bismark_hisat @@ -187,10 +189,7 @@ workflow METHYLSEQ { ch_bwamem_inputs.fasta, ch_bwamem_inputs.fasta_index, ch_bwamem_inputs.bwamem_index, - params.skip_deduplication, - workflow.profile.tokenize(',').intersect(['gpu']).size() >= 1, - // [[],[]], // interval file - // [[],[]] // known sites file + params.skip_deduplication ) ch_bam = FASTQ_ALIGN_DEDUP_BWAMEM.out.bam @@ -233,7 +232,7 @@ workflow METHYLSEQ { // // Subworkflow: Count negative C->T conversion rates as a readout for DNA methylation // - else if (!params.taps && (params.aligner == 'bwameth' || (params.aligner == 'bwamem'))) { + else if (!params.taps && params.aligner == 'bwameth') { ch_bam_bai = ch_bam.join(ch_bai) ch_methyldackel_inputs = ch_bam_bai @@ -310,31 +309,31 @@ workflow METHYLSEQ { // // Collate and save software versions // - def topic_versions = channel.topic("versions") - .distinct() - .branch { entry -> - versions_file: entry instanceof Path - versions_tuple: true - } + softwareVersionsToYAML(ch_versions) + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_' + 'methylseq_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } - def topic_versions_string = topic_versions.versions_tuple + // + // Topic channel versions - written separately to avoid blocking MULTIQC + // These will be merged into the main versions file on workflow completion + // + channel.topic("versions") + .distinct() + .filter { entry -> !(entry instanceof Path) } .map { process, tool, version -> - [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] - } - .groupTuple(by:0) - .map { process, tool_versions -> - tool_versions.unique().sort() - "${process}:\n${tool_versions.join('\n')}" + def processName = process[process.lastIndexOf(':')+1..-1] + "${processName}:\n ${tool}: ${version}" } - - softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) - .mix(topic_versions_string) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'methylseq_software_' + 'mqc_' + 'versions.yml', + name: 'nf_core_methylseq_topic_versions.yml', sort: true, newLine: true - ).set { ch_collated_versions } + ) // // MODULE: MultiQC @@ -400,6 +399,11 @@ workflow METHYLSEQ { emit: bam = ch_bam // channel: [ val(meta), path(bam) ] bai = ch_bai // channel: [ val(meta), path(bai) ] + rastair_mbias = ch_rastair_mbias // channel: [ val(meta), path(rastair_mbias) ] + rastair_call = ch_rastair_call // channel: [ val(meta), path(rastair_call) ] + methylkit = ch_methylkit // channel: [ val(meta), path(methylkit) ] + mbias = ch_mbias // channel: [ val(meta), path(mbias) ] + bedgraph = ch_bedgraph // channel: [ val(meta), path(bedgraph) ] qualimap = ch_qualimap // channel: [ val(meta), path(qualimap) ] preseq = ch_preseq // channel: [ val(meta), path(preseq) ] multiqc_report = ch_multiqc_report // channel: [ path(multiqc_report.html ) ]