diff --git a/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml index 7ff8a2daa051..024f0afcad8a 100644 --- a/modules/nf-core/kallistobustools/count/environment.yml +++ b/modules/nf-core/kallistobustools/count/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kb-python=0.27.2 + - bioconda::kb-python=0.28.2 diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 036bb35d9aa2..841ea2fea6cc 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_COUNT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - 'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' : + 'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }" input: tuple val(meta), path(reads) @@ -14,11 +14,12 @@ process KALLISTOBUSTOOLS_COUNT { path t1c path t2c val technology + val workflow_mode output: - tuple val(meta), path ("*.count"), emit: count - path "versions.yml" , emit: versions - path "*.count/*/*.mtx" , emit: matrix //Ensure that kallisto finished and produced outputs + tuple val(meta), path ("*.count") , emit: count + path "versions.yml" , emit: versions + path "*.count/*/*.mtx" , emit: matrix //Ensure that kallisto finished and produced outputs when: task.ext.when == null || task.ext.when @@ -27,7 +28,7 @@ process KALLISTOBUSTOOLS_COUNT { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def cdna = t1c ? "-c1 $t1c" : '' - def introns = t2c ? "-c2 $t2c" : '' + def intron = t2c ? "-c2 $t2c" : '' def memory = task.memory.toGiga() - 1 """ kb \\ @@ -36,12 +37,25 @@ process KALLISTOBUSTOOLS_COUNT { -i $index \\ -g $t2g \\ $cdna \\ - $introns \\ + $intron \\ -x $technology \\ + --workflow $workflow_mode \\ $args \\ -o ${prefix}.count \\ - ${reads.join( " " )} \\ - -m ${memory}G + -m ${memory}G \\ + ${reads.join( " " )} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p ${prefix}.count/counts_unfiltered/ + touch ${prefix}.count/counts_unfiltered/cells_x_genes.mtx cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml index 7491248c8aaf..55d5dc6cdc41 100644 --- a/modules/nf-core/kallistobustools/count/meta.yml +++ b/modules/nf-core/kallistobustools/count/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python - licence: MIT License + licence: ["MIT"] input: - meta: type: map @@ -34,16 +34,16 @@ input: pattern: "*t2g.txt" - t1c: type: file - description: kb ref's c1 spliced_t2c file + description: kb ref's c1 cdna_t2c file pattern: "*.{cdna_t2c.txt}" - t2c: type: file - description: kb ref's c2 unspliced_t2c file - pattern: "*.{introns_t2c.txt}" + description: kb ref's c2 intron_t2c file + pattern: "*.{intron_t2c.txt}" - workflow_mode: type: string - description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus" - pattern: "{standard,lamanno,nucleus,kite}" + description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" - technology: type: string description: String value defining the sequencing technology used. diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test b/modules/nf-core/kallistobustools/count/tests/main.nf.test new file mode 100644 index 000000000000..550001f925e7 --- /dev/null +++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test @@ -0,0 +1,98 @@ +nextflow_process { + + name "Test Process KALLISTOBUSTOOLS_COUNT" + script "../main.nf" + process "KALLISTOBUSTOOLS_COUNT" + + tag "modules" + tag "modules_nfcore" + tag "kallistobustools" + tag "kallistobustools/count" + tag "kallistobustools/ref" + + setup { + run("KALLISTOBUSTOOLS_REF") { + script "../../ref/main.nf" + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + input[2] = "standard" + """ + } + } + } + + test("genome.fasta + genome.gtf + '10X3' + 'standard'") { + + when { + process { + """ + input[0] = Channel.of( + [ + [id:'test'], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz', checkIfExists: true) + ] + ] + ) + input[1] = KALLISTOBUSTOOLS_REF.out.index + input[2] = KALLISTOBUSTOOLS_REF.out.t2g + input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed. + input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed. + input[5] = "10XV3" + input[6] = "standard" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + process.out.matrix, + path(process.out.count.get(0).get(1)).list().findAll { file(it.toString()).name != "run_info.json" && file(it.toString()).name != "kb_info.json" }, + file(path(process.out.count.get(0).get(1)).list().find { file(it.toString()).name == "kb_info.json" }.toString()).readLines()[15..22], + file(path(process.out.count.get(0).get(1)).list().find { file(it.toString()).name == "run_info.json" }.toString()).readLines()[0..9] + ).match() + } + ) + } + } + + test("genome.fasta + genome.gtf + '10X3' + 'standard' - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of( + [ + [id:'test'], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz', checkIfExists: true) + ] + ] + ) + input[1] = KALLISTOBUSTOOLS_REF.out.index + input[2] = KALLISTOBUSTOOLS_REF.out.t2g + input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed. + input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed. + input[5] = "10XV3" + input[6] = "standard" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap new file mode 100644 index 000000000000..3378c3c16fa5 --- /dev/null +++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "genome.fasta + genome.gtf + '10X3' + 'standard' - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "1": [ + "versions.yml:md5,6ec06270afe0a7572c41567160d927d9" + ], + "2": [ + "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "count": [ + [ + { + "id": "test" + }, + [ + [ + "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "matrix": [ + "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,6ec06270afe0a7572c41567160d927d9" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-01T15:48:45.775904562" + }, + "genome.fasta + genome.gtf + '10X3' + 'standard'": { + "content": [ + [ + "versions.yml:md5,6ec06270afe0a7572c41567160d927d9" + ], + [ + "cells_x_genes.mtx:md5,e12a45e7f7d6527f698dd9cb2e99ecd1" + ], + [ + "10x_version3_whitelist.txt:md5,3d36d0a4021fd292b265e2b5e72aaaf3", + [ + "cells_x_genes.barcodes.txt:md5,41f7adaf43b60f2f4f62d6a7073688de", + "cells_x_genes.genes.names.txt:md5,b29afa75be300c7f24fbd0740a66689b", + "cells_x_genes.genes.txt:md5,fe6d5501923867b514a0447aa4b4995f", + "cells_x_genes.mtx:md5,e12a45e7f7d6527f698dd9cb2e99ecd1" + ], + "inspect.json:md5,bafb47a58ac1bbf9be953f21c361d266", + "matrix.ec:md5,31a4c1a3e8e0c562b12f6569ffbf5459", + "output.bus:md5,d6fa0612a4a16eaf8a3e08bdc13ff49c", + "output.unfiltered.bus:md5,bf899b967657f612ba864188868d58cc", + "transcripts.txt:md5,23861cf43033e7c596e6989a88a3a373" + ], + [ + " \"commands\": [", + " \"kallisto bus -i kb_ref_out.idx -o test.count -x 10XV3 -t 2 subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz\",", + " \"bustools sort -o test.count/tmp/output.s.bus -T test.count/tmp -t 2 -m 2G test.count/output.bus\",", + " \"bustools inspect -o test.count/inspect.json -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",", + " \"bustools correct -o test.count/tmp/output.s.c.bus -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",", + " \"bustools sort -o test.count/output.unfiltered.bus -T test.count/tmp -t 2 -m 2G test.count/tmp/output.s.c.bus\",", + " \"bustools count -o test.count/counts_unfiltered/cells_x_genes -g t2g.txt -e test.count/matrix.ec -t test.count/transcripts.txt --genecounts --umi-gene test.count/output.unfiltered.bus\"", + " ]," + ], + [ + "{", + "\t\"n_targets\": 12,", + "\t\"n_bootstraps\": 0,", + "\t\"n_processed\": 10000,", + "\t\"n_pseudoaligned\": 26,", + "\t\"n_unique\": 26,", + "\t\"p_pseudoaligned\": 0.3,", + "\t\"p_unique\": 0.3,", + "\t\"kallisto_version\": \"0.50.1\",", + "\t\"index_version\": 13," + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-01T15:48:24.476953631" + } +} \ No newline at end of file diff --git a/modules/nf-core/kallistobustools/count/tests/nextflow.config b/modules/nf-core/kallistobustools/count/tests/nextflow.config new file mode 100644 index 000000000000..7a5cbfb441ac --- /dev/null +++ b/modules/nf-core/kallistobustools/count/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: KALLISTOBUSTOOLS_COUNT { + ext.args = '--cellranger -m 1' + } +} diff --git a/modules/nf-core/kallistobustools/count/tests/tags.yml b/modules/nf-core/kallistobustools/count/tests/tags.yml new file mode 100644 index 000000000000..9c4320718c6d --- /dev/null +++ b/modules/nf-core/kallistobustools/count/tests/tags.yml @@ -0,0 +1,2 @@ +kallistobustools/count: + - "modules/nf-core/kallistobustools/count/**" diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml index acbd0e0ad52e..6ae07a8c395f 100644 --- a/modules/nf-core/kallistobustools/ref/environment.yml +++ b/modules/nf-core/kallistobustools/ref/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::kb-python=0.27.2 + - bioconda::kb-python=0.28.2 - conda-forge::requests>=2.23.0 diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 68d72ca9608c..0b45203d029d 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_REF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - 'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' : + 'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }" input: path fasta @@ -62,4 +62,32 @@ process KALLISTOBUSTOOLS_REF { END_VERSIONS """ } + + stub: + if (workflow_mode == "standard") { + """ + touch kb_ref_out.idx \\ + touch t2g.txt \\ + touch cdna.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS + """ + } else { + """ + touch kb_ref_out.idx \\ + touch t2g.txt \\ + touch cdna.fa + touch intron.fa \\ + touch cdna_t2c.txt \\ + touch intron_t2c.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//') + END_VERSIONS + """ + } } diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml index 00be51431d86..64deab9b53d9 100644 --- a/modules/nf-core/kallistobustools/ref/meta.yml +++ b/modules/nf-core/kallistobustools/ref/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python doi: "10.22002/D1.1876" - licence: MIT License + licence: ["MIT"] input: - fasta: type: file @@ -26,8 +26,8 @@ input: pattern: "*.{gtf,gtf.gz}" - workflow_mode: type: string - description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus" - pattern: "{standard,lamanno,nucleus}" + description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" output: - versions: type: file @@ -43,19 +43,19 @@ output: pattern: "*t2g.{txt}" - cdna: type: file - description: Cdna fasta file + description: cDNA fasta file pattern: "*cdna.{fa}" - intron: type: file - description: intron fasta file + description: Intron fasta file pattern: "*intron.{fa}" - cdna_t2c: type: file - description: cdna transcript to capture file + description: cDNA transcript to capture file pattern: "*cdna_t2c.{txt}" - intron_t2c: type: file - description: intron transcript to capture file + description: Intron transcript to capture file pattern: "*intron_t2c.{txt}" authors: - "@flowuenne" diff --git a/modules/nf-core/kallistobustools/ref/tests/main.nf.test b/modules/nf-core/kallistobustools/ref/tests/main.nf.test new file mode 100644 index 000000000000..dc49d9ac5b95 --- /dev/null +++ b/modules/nf-core/kallistobustools/ref/tests/main.nf.test @@ -0,0 +1,120 @@ +nextflow_process { + + name "Test Process KALLISTOBUSTOOLS_REF" + script "../main.nf" + process "KALLISTOBUSTOOLS_REF" + + tag "modules" + tag "modules_nfcore" + tag "kallistobustools" + tag "kallistobustools/ref" + + test("genome.fasta + genome.gtf + 'standard'") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + input[2] = "standard" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + process.out.t2g, + process.out.cdna, + process.out.intron, + process.out.cdna_t2c, + process.out.intron_t2c, + ).match() + }, + { assert file(process.out.index.get(0)).exists() } + ) + } + } + + test("genome.fasta + genome.gtf + 'nac'") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + input[2] = "nac" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + process.out.t2g, + process.out.cdna, + process.out.intron, + process.out.cdna_t2c, + process.out.intron_t2c, + ).match() + }, + { assert file(process.out.index.get(0)).exists() } + ) + } + } + + test("genome.fasta + genome.gtf + 'standard' - stub") { + + options "-stub" + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + input[2] = "standard" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("genome.fasta + genome.gtf + 'nac' - stub") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + input[2] = "nac" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + process.out.t2g, + process.out.cdna, + process.out.intron, + process.out.cdna_t2c, + process.out.intron_t2c, + ).match() + }, + { assert file(process.out.index.get(0)).exists() } + ) + } + } +} diff --git a/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap new file mode 100644 index 000000000000..9c2be8a7317c --- /dev/null +++ b/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap @@ -0,0 +1,136 @@ +{ + "genome.fasta + genome.gtf + 'standard'": { + "content": [ + [ + "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1" + ], + [ + "t2g.txt:md5,d1a8a22c59b9cb0bda39c0c9bb3f6afe" + ], + [ + "cdna.fa:md5,7bca59288fab822451de250d2eee48dc" + ], + [ + + ], + [ + + ], + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-29T23:37:43.739374859" + }, + "genome.fasta + genome.gtf + 'nac'": { + "content": [ + [ + "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1" + ], + [ + "t2g.txt:md5,58591306b33bb948bac7b40f346d0cd7" + ], + [ + "cdna.fa:md5,7bca59288fab822451de250d2eee48dc" + ], + [ + "intron.fa:md5,1aad4e3f5d006f495cc6647fa0bbf6ff" + ], + [ + "cdna_t2c.txt:md5,23861cf43033e7c596e6989a88a3a373" + ], + [ + "intron_t2c.txt:md5,fe6d5501923867b514a0447aa4b4995f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-29T23:37:59.436989671" + }, + "genome.fasta + genome.gtf + 'standard' - stub": { + "content": [ + { + "0": [ + "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1" + ], + "1": [ + "kb_ref_out.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "t2g.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "3": [ + "cdna.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "cdna": [ + "cdna.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "cdna_t2c": [ + + ], + "index": [ + "kb_ref_out.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "intron": [ + + ], + "intron_t2c": [ + + ], + "t2g": [ + "t2g.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-29T23:38:09.578411047" + }, + "genome.fasta + genome.gtf + 'nac' - stub": { + "content": [ + [ + "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1" + ], + [ + "t2g.txt:md5,58591306b33bb948bac7b40f346d0cd7" + ], + [ + "cdna.fa:md5,7bca59288fab822451de250d2eee48dc" + ], + [ + "intron.fa:md5,1aad4e3f5d006f495cc6647fa0bbf6ff" + ], + [ + "cdna_t2c.txt:md5,23861cf43033e7c596e6989a88a3a373" + ], + [ + "intron_t2c.txt:md5,fe6d5501923867b514a0447aa4b4995f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-29T23:38:25.355912473" + } +} \ No newline at end of file diff --git a/modules/nf-core/kallistobustools/ref/tests/tags.yml b/modules/nf-core/kallistobustools/ref/tests/tags.yml new file mode 100644 index 000000000000..208c8d274447 --- /dev/null +++ b/modules/nf-core/kallistobustools/ref/tests/tags.yml @@ -0,0 +1,2 @@ +kallistobustools/ref: + - "modules/nf-core/kallistobustools/ref/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e4bd23452f41..8e1bba4025c0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1146,12 +1146,6 @@ jasminesv: jupyternotebook: - modules/nf-core/jupyternotebook/** - tests/modules/nf-core/jupyternotebook/** -kallistobustools/count: - - modules/nf-core/kallistobustools/count/** - - tests/modules/nf-core/kallistobustools/count/** -kallistobustools/ref: - - modules/nf-core/kallistobustools/ref/** - - tests/modules/nf-core/kallistobustools/ref/** kat/hist: - modules/nf-core/kat/hist/** - tests/modules/nf-core/kat/hist/** diff --git a/tests/modules/nf-core/kallistobustools/count/main.nf b/tests/modules/nf-core/kallistobustools/count/main.nf deleted file mode 100644 index c541b10b989e..000000000000 --- a/tests/modules/nf-core/kallistobustools/count/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { KALLISTOBUSTOOLS_REF } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf' -include { KALLISTOBUSTOOLS_COUNT } from '../../../../../modules/nf-core/kallistobustools/count/main.nf' - -workflow test_kallistobustools_count { - - input = [ - [id:'test'], // meta map - [ - file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_10k_pbmc_cmo_gex1_fastq_1_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_10k_pbmc_cmo_gex1_fastq_2_gz'], checkIfExists: true) - ] - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - sc_workflow = "standard" - technology = "10XV3" - - KALLISTOBUSTOOLS_REF(fasta, gtf, sc_workflow) - KALLISTOBUSTOOLS_COUNT ( - input, - KALLISTOBUSTOOLS_REF.out.index, - KALLISTOBUSTOOLS_REF.out.t2g, - KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed. - KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed. - technology - ) -} diff --git a/tests/modules/nf-core/kallistobustools/count/nextflow.config b/tests/modules/nf-core/kallistobustools/count/nextflow.config deleted file mode 100644 index eacd1e3a78cb..000000000000 --- a/tests/modules/nf-core/kallistobustools/count/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: KALLISTOBUSTOOLS_COUNT { - ext.args = '--cellranger -m 1 --workflow standard' - } - -} diff --git a/tests/modules/nf-core/kallistobustools/count/test.yml b/tests/modules/nf-core/kallistobustools/count/test.yml deleted file mode 100644 index ec985071e413..000000000000 --- a/tests/modules/nf-core/kallistobustools/count/test.yml +++ /dev/null @@ -1,32 +0,0 @@ -- name: kallistobustools count test_kallistobustools_count - command: nextflow run ./tests/modules/nf-core/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/count/nextflow.config - tags: - - kallistobustools/count - - kallistobustools - files: - - path: output/kallistobustools/cdna.fa - - path: output/kallistobustools/kb_ref_out.idx - - path: output/kallistobustools/t2g.txt - - path: output/kallistobustools/test.count/10x_version3_whitelist.txt - md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3 - - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv - md5sum: 2889825ad9c096ca567e057d8ddea098 - - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv - md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14 - - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx - md5sum: b167312e8269d6bbfd609e9cdde837c7 - - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt - md5sum: cf482bc1373075aff0fda0365dfaf3c8 - - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt - md5sum: fe6d5501923867b514a0447aa4b4995f - - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx - md5sum: fc1fe0cbc931e084546d8cb897e50ecc - - path: output/kallistobustools/test.count/inspect.json - md5sum: 0bfebc754e0be8aac2b50bacb52a2541 - - path: output/kallistobustools/test.count/kb_info.json - - path: output/kallistobustools/test.count/matrix.ec - - path: output/kallistobustools/test.count/output.bus - - path: output/kallistobustools/test.count/output.unfiltered.bus - - path: output/kallistobustools/test.count/run_info.json - - path: output/kallistobustools/test.count/transcripts.txt - - path: output/kallistobustools/versions.yml diff --git a/tests/modules/nf-core/kallistobustools/ref/main.nf b/tests/modules/nf-core/kallistobustools/ref/main.nf deleted file mode 100644 index 72bcd2d632a9..000000000000 --- a/tests/modules/nf-core/kallistobustools/ref/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { KALLISTOBUSTOOLS_REF } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf' - -workflow test_kallistobustools_ref_standard { - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - workflow = "standard" - - KALLISTOBUSTOOLS_REF(fasta, gtf, workflow) -} - -workflow test_kallistobustools_ref_lamanno { - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - workflow = "lamanno" - - KALLISTOBUSTOOLS_REF( fasta, gtf, workflow) -} - -workflow test_kallistobustools_ref_nucleus { - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - workflow = "nucleus" - - KALLISTOBUSTOOLS_REF( fasta, gtf, workflow) -} - diff --git a/tests/modules/nf-core/kallistobustools/ref/nextflow.config b/tests/modules/nf-core/kallistobustools/ref/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/kallistobustools/ref/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/kallistobustools/ref/test.yml b/tests/modules/nf-core/kallistobustools/ref/test.yml deleted file mode 100644 index 979c5c32037c..000000000000 --- a/tests/modules/nf-core/kallistobustools/ref/test.yml +++ /dev/null @@ -1,35 +0,0 @@ -- name: kallistobustools ref test_kallistobustools_ref_standard - command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_standard -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config - tags: - - kallistobustools/ref - - kallistobustools - files: - - path: output/kallistobustools/cdna.fa - - path: output/kallistobustools/kb_ref_out.idx - - path: output/kallistobustools/t2g.txt - -- name: kallistobustools ref test_kallistobustools_ref_lamanno - command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config - tags: - - kallistobustools/ref - - kallistobustools - files: - - path: output/kallistobustools/cdna.fa - - path: output/kallistobustools/cdna_t2c.txt - - path: output/kallistobustools/intron.fa - - path: output/kallistobustools/intron_t2c.txt - - path: output/kallistobustools/kb_ref_out.idx - - path: output/kallistobustools/t2g.txt - -- name: kallistobustools ref test_kallistobustools_ref_nucleus - command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config - tags: - - kallistobustools/ref - - kallistobustools - files: - - path: output/kallistobustools/cdna.fa - - path: output/kallistobustools/cdna_t2c.txt - - path: output/kallistobustools/intron.fa - - path: output/kallistobustools/intron_t2c.txt - - path: output/kallistobustools/kb_ref_out.idx - - path: output/kallistobustools/t2g.txt