diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf index e85ddb79..6e085f9b 100644 --- a/modules/star/align/main.nf +++ b/modules/star/align/main.nf @@ -12,11 +12,11 @@ process STAR_ALIGN { saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } // Note: 2.7X indices incompatible with AWS iGenomes. - conda (params.enable_conda ? 'bioconda::star=2.6.1d' : null) + conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container 'https://depot.galaxyproject.org/singularity/star:2.6.1d--0' + container 'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' } else { - container 'quay.io/biocontainers/star:2.6.1d--0' + container 'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' } input: diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf index b440b415..9335b9b5 100644 --- a/modules/star/genomegenerate/main.nf +++ b/modules/star/genomegenerate/main.nf @@ -12,11 +12,11 @@ process STAR_GENOMEGENERATE { saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } // Note: 2.7X indices incompatible with AWS iGenomes. - conda (params.enable_conda ? "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.13 conda-forge::gawk=5.1.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0" + container "https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0" } else { - container "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0" + container "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0" } input: diff --git a/tests/modules/star/align/main.nf b/tests/modules/star/align/main.nf index d280aeae..2a68d7cd 100644 --- a/tests/modules/star/align/main.nf +++ b/tests/modules/star/align/main.nf @@ -2,28 +2,43 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) -include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] ) +include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] ) +include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] ) +include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'] ) + workflow test_star_alignment_single_end { input = [ [ id:'test', single_end:true ], // meta map - [ file("${launchDir}/tests/data/generic/fastq/test_single_end.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] ] - fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) - + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf ) } workflow test_star_alignment_paired_end { input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ] ] - fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) - gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", 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) STAR_GENOMEGENERATE ( fasta, gtf ) STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf ) } + + +workflow test_star_alignment_paired_end_for_fusion { + input = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_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) + + STAR_GENOMEGENERATE ( fasta, gtf ) + STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf ) +} diff --git a/tests/modules/star/align/test.yml b/tests/modules/star/align/test.yml index d6bfb7fa..87413c2c 100644 --- a/tests/modules/star/align/test.yml +++ b/tests/modules/star/align/test.yml @@ -1,73 +1,132 @@ -- name: star align single-end - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config +- name: star align test_star_alignment_single_end + command: nextflow run tests/modules/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config tags: - star - star/align files: - - path: output/star/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: output/star/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: output/star/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: output/star/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: output/star/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: output/star/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: output/star/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: output/star/star/genomeParameters.txt - md5sum: 05e1041cbfb7f81686e17bc80b3ddcea - - path: output/star/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/index/star/Genome + md5sum: a654229fbca6071dcb6b01ce7df704da + - path: output/index/star/Log.out + - path: output/index/star/SA + md5sum: 8c3edc46697b72c9e92440d4cf43506c + - path: output/index/star/SAindex + md5sum: 2a0c675d8b91d8e5e8c1826d3500482e + - path: output/index/star/chrLength.txt + md5sum: c81f40f27e72606d7d07097c1d56a5b5 + - path: output/index/star/chrName.txt + md5sum: 5ae68a67b70976ee95342a7451cb5af1 + - path: output/index/star/chrNameLength.txt + md5sum: b190587cae0531f3cf25552d8aa674db + - path: output/index/star/chrStart.txt + md5sum: 8d3291e6bcdbe9902fbd7c887494173f + - path: output/index/star/exonGeTrInfo.tab + md5sum: d04497f69d6ef889efd4d34fe63edcc4 + - path: output/index/star/exonInfo.tab + md5sum: 0d560290fab688b7268d88d5494bf9fe + - path: output/index/star/geneInfo.tab + md5sum: 8b608537307443ffaee4927d2b428805 + - path: output/index/star/genomeParameters.txt + md5sum: 3097677f4d8b2cb66770b9e55d343a7f + - path: output/index/star/sjdbInfo.txt + md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 + - path: output/index/star/sjdbList.fromGTF.out.tab + md5sum: 8760c33e966dad0b39f440301ebbdee4 + - path: output/index/star/sjdbList.out.tab + md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 + - path: output/index/star/transcriptInfo.tab + md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - path: output/star/test.Aligned.out.bam - md5sum: b7f113f12ff62e09d16fa0ace290d03e + md5sum: 509d7f1fba3350913c8ea13f01917085 + - path: output/star/test.Log.final.out + - path: output/star/test.Log.out + - path: output/star/test.Log.progress.out - path: output/star/test.SJ.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e -- name: star align paired-end - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config +- name: star align test_star_alignment_paired_end + command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config tags: - star - star/align files: - - path: output/star/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: output/star/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: output/star/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: output/star/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: output/star/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: output/star/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: output/star/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: output/star/star/genomeParameters.txt - md5sum: 05e1041cbfb7f81686e17bc80b3ddcea - - path: output/star/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/star/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/index/star/Genome + md5sum: a654229fbca6071dcb6b01ce7df704da + - path: output/index/star/Log.out + - path: output/index/star/SA + md5sum: 8c3edc46697b72c9e92440d4cf43506c + - path: output/index/star/SAindex + md5sum: 2a0c675d8b91d8e5e8c1826d3500482e + - path: output/index/star/chrLength.txt + md5sum: c81f40f27e72606d7d07097c1d56a5b5 + - path: output/index/star/chrName.txt + md5sum: 5ae68a67b70976ee95342a7451cb5af1 + - path: output/index/star/chrNameLength.txt + md5sum: b190587cae0531f3cf25552d8aa674db + - path: output/index/star/chrStart.txt + md5sum: 8d3291e6bcdbe9902fbd7c887494173f + - path: output/index/star/exonGeTrInfo.tab + md5sum: d04497f69d6ef889efd4d34fe63edcc4 + - path: output/index/star/exonInfo.tab + md5sum: 0d560290fab688b7268d88d5494bf9fe + - path: output/index/star/geneInfo.tab + md5sum: 8b608537307443ffaee4927d2b428805 + - path: output/index/star/genomeParameters.txt + md5sum: 3097677f4d8b2cb66770b9e55d343a7f + - path: output/index/star/sjdbInfo.txt + md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 + - path: output/index/star/sjdbList.fromGTF.out.tab + md5sum: 8760c33e966dad0b39f440301ebbdee4 + - path: output/index/star/sjdbList.out.tab + md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 + - path: output/index/star/transcriptInfo.tab + md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - path: output/star/test.Aligned.out.bam - md5sum: a1f92e8dbeb954b6b8d3d7cc6b9814fb + md5sum: 64b408fb1d61e2de8ff51c847cd5bc52 + - path: output/star/test.Log.final.out + - path: output/star/test.Log.out + - path: output/star/test.Log.progress.out - path: output/star/test.SJ.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e + +- name: star align test_star_alignment_paired_end_for_fusion + command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c tests/config/nextflow.config + tags: + - star + - star/align + files: + - path: output/index/star/Genome + md5sum: a654229fbca6071dcb6b01ce7df704da + - path: output/index/star/Log.out + - path: output/index/star/SA + md5sum: 8c3edc46697b72c9e92440d4cf43506c + - path: output/index/star/SAindex + md5sum: 2a0c675d8b91d8e5e8c1826d3500482e + - path: output/index/star/chrLength.txt + md5sum: c81f40f27e72606d7d07097c1d56a5b5 + - path: output/index/star/chrName.txt + md5sum: 5ae68a67b70976ee95342a7451cb5af1 + - path: output/index/star/chrNameLength.txt + md5sum: b190587cae0531f3cf25552d8aa674db + - path: output/index/star/chrStart.txt + md5sum: 8d3291e6bcdbe9902fbd7c887494173f + - path: output/index/star/exonGeTrInfo.tab + md5sum: d04497f69d6ef889efd4d34fe63edcc4 + - path: output/index/star/exonInfo.tab + md5sum: 0d560290fab688b7268d88d5494bf9fe + - path: output/index/star/geneInfo.tab + md5sum: 8b608537307443ffaee4927d2b428805 + - path: output/index/star/genomeParameters.txt + md5sum: 3097677f4d8b2cb66770b9e55d343a7f + - path: output/index/star/sjdbInfo.txt + md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 + - path: output/index/star/sjdbList.fromGTF.out.tab + md5sum: 8760c33e966dad0b39f440301ebbdee4 + - path: output/index/star/sjdbList.out.tab + md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 + - path: output/index/star/transcriptInfo.tab + md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 + - path: output/star/test.Aligned.out.bam + md5sum: d724ca90a102347b9c5052a33ea4d308 + - path: output/star/test.Log.final.out + - path: output/star/test.Log.out + - path: output/star/test.Log.progress.out + - path: output/star/test.SJ.out.tab + md5sum: 5155c9fd1f787ad6d7d80987fb06219c diff --git a/tests/modules/star/genomegenerate/test.yml b/tests/modules/star/genomegenerate/test.yml index 4e9c2247..0a4bff80 100644 --- a/tests/modules/star/genomegenerate/test.yml +++ b/tests/modules/star/genomegenerate/test.yml @@ -1,31 +1,37 @@ -- name: star genomegenerate - command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config +- name: star genomegenerate test_star_genomegenerate + command: nextflow run tests/modules/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config tags: - - star - star/genomegenerate + - star files: - - path: ./output/index/star/Genome - md5sum: 323c992bac354f93073ce0fc43f222f8 - - path: ./output/index/star/SA - md5sum: 3e70e4fc6d031e1915bb510727f2c559 - - path: ./output/index/star/SAindex - md5sum: a94198b95a245d4f64af2a7133b6ec7b - - path: ./output/index/star/chrLength.txt - md5sum: f2bea3725fe1c01420c57fb73bdeb31a - - path: ./output/index/star/chrNameLength.txt - md5sum: c7ceb0a8827b2ea91c386933bee48742 - - path: ./output/index/star/chrStart.txt - md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: ./output/index/star/exonGeTrInfo.tab - md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - - path: ./output/index/star/exonInfo.tab - md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - - path: ./output/index/star/sjdbInfo.txt - md5sum: 1082ab459363b3f2f7aabcef0979c1ed - - path: ./output/index/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: ./output/index/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: ./output/index/star/transcriptInfo.tab - md5sum: 8fbe69abbbef4f89da3854873984dbac - - path: ./output/index/star/genomeParameters.txt + - path: output/index/star/Genome + md5sum: a654229fbca6071dcb6b01ce7df704da + - path: output/index/star/Log.out + - path: output/index/star/SA + md5sum: 8c3edc46697b72c9e92440d4cf43506c + - path: output/index/star/SAindex + md5sum: d0fbf2789ee1e9f60c352ba3655d9de4 + - path: output/index/star/chrLength.txt + md5sum: c81f40f27e72606d7d07097c1d56a5b5 + - path: output/index/star/chrName.txt + md5sum: 5ae68a67b70976ee95342a7451cb5af1 + - path: output/index/star/chrNameLength.txt + md5sum: b190587cae0531f3cf25552d8aa674db + - path: output/index/star/chrStart.txt + md5sum: 8d3291e6bcdbe9902fbd7c887494173f + - path: output/index/star/exonGeTrInfo.tab + md5sum: d04497f69d6ef889efd4d34fe63edcc4 + - path: output/index/star/exonInfo.tab + md5sum: 0d560290fab688b7268d88d5494bf9fe + - path: output/index/star/geneInfo.tab + md5sum: 8b608537307443ffaee4927d2b428805 + - path: output/index/star/genomeParameters.txt + md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d + - path: output/index/star/sjdbInfo.txt + md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 + - path: output/index/star/sjdbList.fromGTF.out.tab + md5sum: 8760c33e966dad0b39f440301ebbdee4 + - path: output/index/star/sjdbList.out.tab + md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 + - path: output/index/star/transcriptInfo.tab + md5sum: 0c3a5adb49d15e5feff81db8e29f2e36