From 4b9de286018cb2ba1d51ae9a4860387123b26cd2 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Thu, 15 Aug 2024 22:56:45 +0200 Subject: [PATCH 1/2] Updated mkfastq and removed customdumpsoftware from modules.json --- conf/modules.config | 9 +- conf/test_mkfastq.config | 4 +- modules.json | 89 +++++++++++++------ modules/nf-core/cellranger/mkfastq/main.nf | 24 +++-- .../cellranger/mkfastq/tests/main.nf.test | 3 + .../mkfastq/tests/main.nf.test.snap | 41 +++++++-- tests/pipeline/mkfastq.nf.test | 29 +++--- tests/pipeline/mkfastq.nf.test.snap | 31 ++++--- 8 files changed, 164 insertions(+), 66 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e0d1c766..6d635d07 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -203,7 +203,14 @@ process { //Gather fastqs path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, - pattern: "**/outs/fastq_path/**.fastq.gz", + pattern: "**/outs/fastq_path/**/*.fastq.gz", + saveAs: {filename -> filename.split("/")[-1] } + ], + [ + //Gather undetermined fastqs + path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}/undetermined" : "${params.outdir}/${meta.id}/undetermined" }, + mode: params.publish_dir_mode, + pattern: "**/outs/fastq_path/*.fastq.gz", saveAs: {filename -> filename.split("/")[-1] } ] ] diff --git a/conf/test_mkfastq.config b/conf/test_mkfastq.config index 7990e1c8..7940f14d 100644 --- a/conf/test_mkfastq.config +++ b/conf/test_mkfastq.config @@ -20,7 +20,7 @@ params { max_time = '1.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/mkfastq-samplesheet.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/cellranger_tiny/mkfastq_tiny_samplesheet.csv' demultiplexer = 'mkfastq' - skip_tools = 'samshee' + skip_tools = 'samshee,falco' } diff --git a/modules.json b/modules.json index 2bf52fe9..33a290bc 100644 --- a/modules.json +++ b/modules.json @@ -8,82 +8,107 @@ "bases2fastq": { "branch": "master", "git_sha": "c651992bf8425fecefe14085ff486f42172cba77", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcl2fastq": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": ["bcl_demultiplex"] + "installed_by": [ + "bcl_demultiplex" + ] }, "bclconvert": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": ["bcl_demultiplex"] + "installed_by": [ + "bcl_demultiplex" + ] }, "cellranger/mkfastq": { "branch": "master", - "git_sha": "d89faad13503f47372b8706008f7cdb2c4f1d859", - "installed_by": ["modules"] + "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257", + "installed_by": [ + "modules" + ] }, "checkqc": { "branch": "master", "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731", - "installed_by": ["modules"] - }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "falco": { "branch": "master", "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastp": { "branch": "master", "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fqtk": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kraken2/kraken2": { "branch": "master", "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", - "installed_by": ["fastq_contam_seqtk_kraken"] + "installed_by": [ + "fastq_contam_seqtk_kraken" + ] }, "md5sum": { "branch": "master", "git_sha": "1164836d4d3922ab937865b17086485f0f472748", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/sample": { "branch": "master", "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", - "installed_by": ["fastq_contam_seqtk_kraken"] + "installed_by": [ + "fastq_contam_seqtk_kraken" + ] }, "sgdemux": { "branch": "master", "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -92,30 +117,40 @@ "bcl_demultiplex": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "fastq_contam_seqtk_kraken": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf index ab03f984..06c15bbc 100644 --- a/modules/nf-core/cellranger/mkfastq/main.nf +++ b/modules/nf-core/cellranger/mkfastq/main.nf @@ -8,11 +8,12 @@ process CELLRANGER_MKFASTQ { tuple val(meta), path(csv), path(bcl) output: - tuple val(meta), path("*_outs/outs/fastq_path/*.fastq.gz"), emit: fastq - tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports - tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats - tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop - path "versions.yml" , emit: versions + tuple val(meta), path("*_outs/outs/fastq_path/**/*.fastq.gz") , emit: fastq + tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq + tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports + tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats + tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -47,8 +48,8 @@ process CELLRANGER_MKFASTQ { } def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir -p "${prefix}_outs/outs/fastq_path/" - # data with something to avoid breaking nf-test java I/O stream + mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/" + # data with something to avoid breaking nf-test java I/O stream, fastq cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/fake_file.fastq @SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT @@ -57,6 +58,15 @@ process CELLRANGER_MKFASTQ { FAKE_FQ gzip -n ${prefix}_outs/outs/fastq_path/fake_file.fastq + # data with something to avoid breaking nf-test java I/O stream, fastq_undetermined + cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq + @SEQ_ID + GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + + + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 + FAKE_FQ + gzip -n ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq + # data for reports output channel mkdir -p "${prefix}_outs/outs/fastq_path/Reports" diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test index 8aee4001..8d3d718f 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() @@ -65,6 +66,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() @@ -91,6 +93,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap index e539f8e2..b1224688 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap @@ -1,6 +1,19 @@ { "cellranger - tiny - simple": { "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2" + ] + ] + ], [ [ { @@ -28,10 +41,10 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:45:20.493024717" + "timestamp": "2024-08-15T19:59:53.012035" }, "cellranger - tiny - simple - stub": { "content": [ @@ -43,6 +56,9 @@ }, "fake_file.fastq.gz:md5,8e16c1f4a441cbb3b7de374d2c924da7" ] + ], + [ + ], [ [ @@ -58,13 +74,26 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:47:11.995685118" + "timestamp": "2024-08-15T20:01:48.013075" }, "cellranger - tiny - illumina": { "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2" + ] + ] + ], [ [ { @@ -92,9 +121,9 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:46:17.031302052" + "timestamp": "2024-08-15T20:01:00.558148" } } \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 885dff9e..96e57a5d 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -18,25 +18,32 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 7 }, + { assert workflow.trace.succeeded().size() == 10 }, // How many directories were produced? {assert path("${outputDir}").list().size() == 6}, // How many files were produced? - {assert path("$outputDir/220422_M11111_0222_000000000-K9H97_mkfastq/").list().size() == 2}, + {assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2}, {assert path("$outputDir/multiqc/").list().size() == 3}, {assert path("$outputDir/pipeline_info/").list().size() == 5}, // File assertions: Files that should be exactly the same with every pipeline execution. {assert snapshot( //Check output files - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_summary.txt"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_report.html").exists(), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_fastqc_data.txt"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.json"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.html").exists(), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/InterOp/IndexMetricsOut.bin") + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"), + path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin") ).match("file_assertions_mkfastq")} ) } diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index 6b200b57..90f53dc4 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -1,30 +1,37 @@ { "software_versions": { "content": [ - "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}" + "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}" ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.3" }, - "timestamp": "2024-08-02T20:09:53.707554042" + "timestamp": "2024-08-15T17:36:35.551329" }, "file_assertions_mkfastq": { "content": [ - "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", + "test_sample_S1_L001_1.fastp.fastq.gz:md5,b348491a3b1afa096fde514dbdf55215", + "test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236", + "test_sample_S1_L001_2.fastp.fastq.gz:md5,1c60f1f3958b8b2b0255b9fae6df0b3d", + "test_sample_S1_L001_2.fastp.fastq.gz.md5:md5,01d742cc56639c476b0bac0c094eba4b", + "test_sample_S1_L001_I1_001.fastp.fastq.gz.md5:md5,82e397b4a2418f27269a30f6ca0e349e", + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2", + "Undetermined_S0_L001_I1_001.fastq.gz:md5,c93946d67bdb1d5b2ab955fd1dc9cb31", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,faa79ce215ae72fdc3375cda066c6757", + "Undetermined_S0_L001_R2_001.fastq.gz:md5,d8955db4dfbf7aee89b6bdc3b7629f8f", true, - "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", - "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001.fastp.json:md5,ed62c667631b03f5fd3b50454322b423", true, - "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", - "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf" + "test_sample_S1_L001.fastp.json:md5,f616058446c5822797048ea6c5d2393d", + "test_sample_S1_L001_I1_001.fastp.json:md5,42cad4ed99a3d577f100017cbe11d711", + "IndexMetricsOut.bin:md5,e2ac28695537336b53a509f48e93ed1f" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-23T23:50:42.910185053" + "timestamp": "2024-08-15T17:54:45.551098" } -} +} \ No newline at end of file From 452e91814c1aebc85f8cad4245f25d140cd86c87 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Thu, 15 Aug 2024 21:00:05 +0000 Subject: [PATCH 2/2] Ran pre-commit --- modules.json | 82 +++++++++------------------------- tests/pipeline/mkfastq.nf.test | 2 +- 2 files changed, 22 insertions(+), 62 deletions(-) diff --git a/modules.json b/modules.json index 33a290bc..8138d097 100644 --- a/modules.json +++ b/modules.json @@ -8,107 +8,77 @@ "bases2fastq": { "branch": "master", "git_sha": "c651992bf8425fecefe14085ff486f42172cba77", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcl2fastq": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": [ - "bcl_demultiplex" - ] + "installed_by": ["bcl_demultiplex"] }, "bclconvert": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": [ - "bcl_demultiplex" - ] + "installed_by": ["bcl_demultiplex"] }, "cellranger/mkfastq": { "branch": "master", "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "checkqc": { "branch": "master", "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "falco": { "branch": "master", "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fqtk": { "branch": "master", "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kraken2/kraken2": { "branch": "master", "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", - "installed_by": [ - "fastq_contam_seqtk_kraken" - ] + "installed_by": ["fastq_contam_seqtk_kraken"] }, "md5sum": { "branch": "master", "git_sha": "1164836d4d3922ab937865b17086485f0f472748", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/sample": { "branch": "master", "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", - "installed_by": [ - "fastq_contam_seqtk_kraken" - ] + "installed_by": ["fastq_contam_seqtk_kraken"] }, "sgdemux": { "branch": "master", "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -117,40 +87,30 @@ "bcl_demultiplex": { "branch": "master", "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_contam_seqtk_kraken": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 96e57a5d..584656b7 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -40,7 +40,7 @@ nextflow_pipeline { path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"), path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"), path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"), path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"), path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin")