From 524a164a3f7a901984db1277e8f2939a509effaa Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 27 Nov 2024 05:22:03 +0000 Subject: [PATCH 1/4] install fasta_index_bismark_bwameth from nf-core --- CHANGELOG.md | 5 +- main.nf | 22 +- modules.json | 15 +- .../local/prepare_genome/tests/main.nf.test | 105 ----- .../prepare_genome/tests/main.nf.test.snap | 145 ------- .../fasta_index_bismark_bwameth}/main.nf | 75 ++-- .../fasta_index_bismark_bwameth/meta.yml | 72 ++++ .../nextflow.config | 0 .../tests/main.nf.test | 227 +++++++++++ .../tests/main.nf.test.snap | 378 ++++++++++++++++++ .../tests/nextflow.config | 5 + workflows/methylseq/nextflow.config | 2 +- 12 files changed, 741 insertions(+), 310 deletions(-) delete mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test delete mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test.snap rename subworkflows/{local/prepare_genome => nf-core/fasta_index_bismark_bwameth}/main.nf (56%) create mode 100644 subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml rename subworkflows/{local/prepare_genome => nf-core/fasta_index_bismark_bwameth}/nextflow.config (100%) create mode 100644 subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test create mode 100644 subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config diff --git a/CHANGELOG.md b/CHANGELOG.md index fcf1a72b..88d17869 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,15 @@ ### Bug fixes & refactoring -- 🐛 fix fasta gunzip output [#457](https://github.com/nf-core/methylseq/pull/457) +- 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457) - 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457) ### Pipeline Updates - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457) +- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/) +- 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/) +- 🔧 reorg individual configs to conf/modules/ named configs [#459](https://github.com/nf-core/methylseq/pull/) ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] diff --git a/main.nf b/main.nf index 5c1056c8..636d0a80 100644 --- a/main.nf +++ b/main.nf @@ -15,11 +15,11 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { METHYLSEQ } from './workflows/methylseq/' -include { PREPARE_GENOME } from './subworkflows/local/prepare_genome/' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { FASTA_INDEX_BISMARK_BWAMETH } from './subworkflows/nf-core/fasta_index_bismark_bwameth/main' +include { METHYLSEQ } from './workflows/methylseq/' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_methylseq_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52,13 +52,13 @@ workflow NFCORE_METHYLSEQ { // // SUBWORKFLOW: Prepare any required reference genome indices // - PREPARE_GENOME( + FASTA_INDEX_BISMARK_BWAMETH( params.fasta, params.fasta_index, params.bismark_index, params.bwameth_index, ) - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + ch_versions = ch_versions.mix(FASTA_INDEX_BISMARK_BWAMETH.out.versions) // // WORKFLOW: Run pipeline @@ -67,10 +67,10 @@ workflow NFCORE_METHYLSEQ { METHYLSEQ ( samplesheet, ch_versions, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_index, - PREPARE_GENOME.out.bismark_index, - PREPARE_GENOME.out.bwameth_index, + FASTA_INDEX_BISMARK_BWAMETH.out.fasta, + FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index, + FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index, + FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index, ) emit: multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html diff --git a/modules.json b/modules.json index 403f0305..4b7d4145 100644 --- a/modules.json +++ b/modules.json @@ -23,7 +23,7 @@ "bismark/genomepreparation": { "branch": "master", "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "bismark/methylationextractor": { "branch": "master", @@ -48,7 +48,7 @@ "bwameth/index": { "branch": "master", "git_sha": "a716d10039f9728f2674f45c33a95b605851ea50", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "cat/fastq": { "branch": "master", @@ -63,7 +63,7 @@ "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "methyldackel/extract": { "branch": "master", @@ -103,7 +103,7 @@ "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "samtools/flagstat": { "branch": "master", @@ -133,12 +133,17 @@ "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] } } }, "subworkflows": { "nf-core": { + "fasta_index_bismark_bwameth": { + "branch": "master", + "git_sha": "e24c9731daae27a4cd0b072f2e50cc8401a492db", + "installed_by": ["subworkflows"] + }, "fastq_align_dedup_bismark": { "branch": "master", "git_sha": "af84433c2e619cf28e026d4140b1b8763ae3690b", diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test deleted file mode 100644 index c7f20b6a..00000000 --- a/subworkflows/local/prepare_genome/tests/main.nf.test +++ /dev/null @@ -1,105 +0,0 @@ -nextflow_workflow { - - name "Test Workflow PREPARE_GENOME" - script "../main.nf" - workflow "PREPARE_GENOME" - config "../nextflow.config" - - test("Generate Bismark Index (bowtie2)") { - - when { - params { - aligner = "bismark" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.bismark_index, - workflow.out.versions - ).match() } - ) - } - - } - - test("Generate Bismark Index (hisat2)") { - - when { - params { - aligner = "bismark_hisat" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.bismark_index, - workflow.out.versions - ).match() } - ) - } - - } - - test("Generate Bwameth Index") { - - when { - params { - aligner = "bwameth" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.fasta_index, - workflow.out.bwameth_index, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap deleted file mode 100644 index 0ba14f1c..00000000 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ /dev/null @@ -1,145 +0,0 @@ -{ - "Generate Bismark Index (hisat2)": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - [ - { - - }, - [ - [ - [ - "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81", - "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018", - "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b", - "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd", - "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee", - "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41", - "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ], - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" - ] - ] - ], - [ - "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" - }, - "timestamp": "2024-11-26T06:16:45.30242884" - }, - "Generate Bwameth Index": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451" - ], - [ - [ - { - - }, - [ - "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", - "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", - "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", - "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", - "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", - "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" - ] - ] - ], - [ - "versions.yml:md5,7303f194674b485c6914e28422822a12", - "versions.yml:md5,cb3f3b6e54f9a7b3b6d4f5f875e89442" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T11:27:38.06274051" - }, - "Generate Bismark Index (bowtie2)": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - [ - { - - }, - [ - [ - [ - "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", - "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", - "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", - "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", - "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ], - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" - ] - ] - ], - [ - "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" - }, - "timestamp": "2024-11-26T06:16:09.122741589" - } -} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf similarity index 56% rename from subworkflows/local/prepare_genome/main.nf rename to subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf index f132b26a..4dd21888 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf @@ -1,29 +1,26 @@ -// -// Prepare reference genome files -// - include { UNTAR } from '../../../modules/nf-core/untar/main' include { GUNZIP } from '../../../modules/nf-core/gunzip/main' include { BISMARK_GENOMEPREPARATION } from '../../../modules/nf-core/bismark/genomepreparation/main' include { BWAMETH_INDEX } from '../../../modules/nf-core/bwameth/index/main' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' -workflow PREPARE_GENOME { +workflow FASTA_INDEX_BISMARK_BWAMETH { + take: - fasta // file: /path/to/genome.fasta - fasta_index // file: /path/to/genome.fasta.fai - bismark_index // directory: /path/to/bismark/index/ - bwameth_index // directory: /path/to/bwameth/index/ + fasta // channel: [ val(meta), [ fasta ] ] + fasta_index // channel: [ val(meta), [ fasta index ] ] + bismark_index // channel: [ val(meta), [ bismark index ] ] + bwameth_index // channel: [ val(meta), [ bwameth index ] ] main: - ch_versions = Channel.empty() + ch_fasta = Channel.empty() ch_fasta_index = Channel.empty() ch_bismark_index = Channel.empty() ch_bwameth_index = Channel.empty() + ch_versions = Channel.empty() - // FASTA, if supplied - if (fasta.endsWith('.gz')) { + if (fasta.toString().endsWith('.gz')) { GUNZIP ( [ [:], file(fasta, checkIfExists: true) ] ) @@ -32,7 +29,6 @@ workflow PREPARE_GENOME { } else { ch_fasta = Channel.value([[:], file(fasta, checkIfExists: true)]) } - ch_fasta.dump(tag: 'PREPARE_GENOME: ch_fasta') // Aligner: bismark or bismark_hisat if( params.aligner =~ /bismark/ ){ @@ -40,46 +36,44 @@ workflow PREPARE_GENOME { * Generate bismark index if not supplied */ if (bismark_index) { - if (bismark_index.endsWith('.gz')) { - ch_bismark_index = UNTAR ([ [:], file(bismark_index) ]).untar - ch_bismark_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bismark_index') - + if (bismark_index.toString().endsWith('.gz')) { + UNTAR ( + [ [:], file(bismark_index, checkIfExists: true) ] + ) + ch_bismark_index = UNTAR.out.untar ch_versions = ch_versions.mix(UNTAR.out.versions) } else { ch_bismark_index = Channel.value([[:], file(bismark_index, checkIfExists: true)]) - ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') } } else { - BISMARK_GENOMEPREPARATION(ch_fasta) - + BISMARK_GENOMEPREPARATION ( + ch_fasta + ) ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index - ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') - ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION.out.versions) } - } + // Aligner: bwameth else if ( params.aligner == 'bwameth' ){ /* * Generate bwameth index if not supplied */ if (bwameth_index) { - if (bwameth_index.endsWith('.tar.gz')) { - ch_bwameth_index = UNTAR ([ [:], file(bwameth_index, checkIfExists: true) ]).untar - ch_bwameth_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bwameth_index') - + if (bwameth_index.toString().endsWith('.gz')) { + UNTAR ( + [ [:], file(bwameth_index, checkIfExists: true) ] + ) + ch_bwameth_index = UNTAR.out.untar ch_versions = ch_versions.mix(UNTAR.out.versions) } else { ch_bwameth_index = Channel.value([[:], file(bwameth_index, checkIfExists: true)]) - ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') } } else { - BWAMETH_INDEX(ch_fasta) - + BWAMETH_INDEX ( + ch_fasta + ) ch_bwameth_index = BWAMETH_INDEX.out.index - ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') - ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions) } @@ -88,24 +82,21 @@ workflow PREPARE_GENOME { */ if (fasta_index) { ch_fasta_index = Channel.value(file(fasta_index, checkIfExists: true)) - ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') } else { SAMTOOLS_FAIDX( ch_fasta, [[:], []] ) - ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])} - ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') - + ch_fasta_index = SAMTOOLS_FAIDX.out.fai ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) } } emit: - fasta = ch_fasta // channel: path(genome.fasta) - bismark_index = ch_bismark_index // channel: path(genome.fasta) - bwameth_index = ch_bwameth_index // channel: path(genome.fasta) - fasta_index = ch_fasta_index // channel: path(genome.fasta) - versions = ch_versions // channel: [ versions.yml ] - + fasta = ch_fasta // channel: [ val(meta), [ fasta ] ] + 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 ] ] + versions = ch_versions // channel: [ versions.yml ] } + diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml new file mode 100644 index 00000000..55854429 --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml @@ -0,0 +1,72 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fasta_index_bismark_bwameth" +description: Generate index files from reference fasta for bismark and bwameth +keywords: + - bismark + - bwameth + - prepare genome + - index +components: + - untar + - gunzip + - bismark/genomepreparation + - bwameth/index + - samtools/faidx +input: + - fasta: + type: file + description: | + Reference genome + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa/fa.gz}" + - fasta_index: + type: file + description: | + Reference genome index file + Structure: [ val(meta), path(fasta) ] + pattern: "*.fai" + - bismark_index: + type: file + description: | + Bismark genome index files + Structure: [ val(meta), path(bismark_index) ] + - bwameth_index: + type: file + description: | + Bwameth genome index files + Structure: [ val(meta), path(bwameth_index) ] +output: + - fasta: + type: file + description: | + Reference genome + Structure: [ val(meta), path(fasta) ] + pattern: "*.fa" + - fasta_index: + type: file + description: | + Reference genome index file + Structure: [ val(meta), path(fasta) ] + pattern: "*.fai" + - bismark_index: + type: file + description: | + Bismark genome index files + Structure: [ val(meta), path(bismark_index) ] + pattern: "BismarkIndex" + - bwameth_index: + type: file + description: | + Bwameth genome index files + Structure: [ val(meta), path(bwameth_index) ] + pattern: "index" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config similarity index 100% rename from subworkflows/local/prepare_genome/nextflow.config rename to subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test new file mode 100644 index 00000000..3219ea6d --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test @@ -0,0 +1,227 @@ +nextflow_workflow { + + name "Test Subworkflow FASTA_INDEX_BISMARK_BWAMETH" + script "../main.nf" + workflow "FASTA_INDEX_BISMARK_BWAMETH" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fasta_index_bismark_bwameth" + tag "untar" + tag "gunzip" + tag "bismark/genomepreparation" + tag "bwameth/index" + tag "samtools/faidx" + + test("Params: bismark | download bismark index (bowtie2)") { + + when { + params { + aligner = "bismark" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark | generate bismark index (bowtie2)") { + + when { + params { + aligner = "bismark" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat | download bismark index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat | generate bismark index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | download fasta index | download bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + input[2] = [] // bismark index + input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | generate fasta index | download bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] //fasta index + input[2] = [] // bismark index + input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | generate fasta index | generate bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = [] // bismark index + input[3] = [] // bwameth index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + +} diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap new file mode 100644 index 00000000..2bb64c16 --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap @@ -0,0 +1,378 @@ +{ + "Params: bismark | download bismark index (bowtie2)": { + "content": [ + [ + [ + { + + }, + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" + ] + ], + [ + + ], + [ + [ + { + + }, + [ + [ + [ + "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", + "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", + 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"genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ], + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" + ] + ] + ], + [ + + ], + [ + "versions.yml:md5,90950cf3155e6a77273de11ebb93a541", + "versions.yml:md5,dc24c245324a3b8a8328f1ed6abd3f7c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-26T16:25:20.094964567" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config new file mode 100644 index 00000000..ba4fa6f6 --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BISMARK_GENOMEPREPARATION { + ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' } + } +} diff --git a/workflows/methylseq/nextflow.config b/workflows/methylseq/nextflow.config index 3eb53510..506311f2 100644 --- a/workflows/methylseq/nextflow.config +++ b/workflows/methylseq/nextflow.config @@ -6,9 +6,9 @@ includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config" includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config" // subworkflow configs +includeConfig "../../subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config" includeConfig "../../subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config" includeConfig "../../subworkflows/local/bwameth/nextflow.config" -includeConfig "../../subworkflows/local/prepare_genome/nextflow.config" process { From 981077cf0ef245a6e9fde94deed059753e00b589 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 27 Nov 2024 05:23:44 +0000 Subject: [PATCH 2/4] --fix files_unchanged --- .github/workflows/linting.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a502573c..dbd52d5a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | From 6b1b3eb30c26c5010c75457294a4648e909efc82 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 27 Nov 2024 05:58:53 +0000 Subject: [PATCH 3/4] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 88d17869..8dd90e75 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457) - 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/) - 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/) -- 🔧 reorg individual configs to conf/modules/ named configs [#459](https://github.com/nf-core/methylseq/pull/) +- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/) ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] From ad6f8bb216a81353333c49a1ea9e667188d5edea Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 27 Nov 2024 07:30:30 +0000 Subject: [PATCH 4/4] fix .github/workflows/linting.yml --- .github/workflows/linting.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index dbd52d5a..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python 3.12 - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: |