From d51a4504dec0f4139ec4ad5f622ce2fc27ac238d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Dec 2024 21:19:22 -0600 Subject: [PATCH] test: That's why STAR is outputting samtools --- conf/modules.config | 23 +++++++++- tests/.nftignore | 2 - workflows/tests/aligner/star.nf.test.snap | 54 +++++++++++------------ 3 files changed, 46 insertions(+), 33 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4e763048..edcf519f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -176,7 +176,7 @@ process { // Alignment post-processing // /////////////////////////////// - withName: '.*:BAM_SORT_STATS_SAMTOOLS:.*|.*:BAM_SORT_STATS_SAMTOOLS_GENOME:.*' { + withName: '.*:BAM_SORT_STATS_SAMTOOLS:.*|.*' { ext.prefix = { "${meta.id}.sorted.bam" } publishDir = [ path: { "${params.outdir}/${params.aligner}/samtools_stats" }, @@ -185,7 +185,7 @@ process { ] } - withName: '.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*|.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_.*' { + withName: '.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*' { ext.prefix = { "${meta.id}.sorted" } publishDir = [ path: { "${params.outdir}/${params.aligner}" }, @@ -194,6 +194,25 @@ process { ] } + withName: ".*:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:.*" { + ext.prefix = {"${meta.id}_genome"} + publishDir = [ + path: { "${params.outdir}/${params.aligner}/samtools_stats" }, + mode: params.publish_dir_mode, + pattern: "*.{stats,flagstat,idxstats}" + ] + } + + withName: ".*:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:.*" { + ext.prefix = {"${meta.id}_transcriptome"} + publishDir = [ + path: { "${params.outdir}/${params.aligner}/samtools_stats" }, + mode: params.publish_dir_mode, + pattern: "*.{stats,flagstat,idxstats}" + ] + } + + if(params.with_umi) { withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS:UMITOOLS_DEDUP' { ext.args = { [ diff --git a/tests/.nftignore b/tests/.nftignore index 909d61c8..af6c7828 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -17,8 +17,6 @@ pipeline_info/*.{html,json,txt,yml} */alignments/logs/*.txt star/log/*.Log.{final.out,out,progress.out} star/star/Log.out -# FIXME idk why star outputs this -samtools/* hisat2/log/*.hisat2.summary.log */deduplicated/logs/*.txt */{reports,summary}/*.{html,txt} diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap index 11bf7eda..1eff98ff 100644 --- a/workflows/tests/aligner/star.nf.test.snap +++ b/workflows/tests/aligner/star.nf.test.snap @@ -234,17 +234,7 @@ "samtools", "samtools/cd4.bam", "samtools/jurkat.bam", - "samtools/jurkat.bam.bai", - "samtools/jurkat.flagstat", - "samtools/jurkat.idxstats", - "samtools/jurkat.stats", "star", - "star/cd4_REP1.sorted.bam", - "star/cd4_REP1.sorted.bam.bai", - "star/cd4_REP2.sorted.bam", - "star/cd4_REP2.sorted.bam.bai", - "star/jurkat.sorted.bam", - "star/jurkat.sorted.bam.bai", "star/log", "star/log/cd4_REP1.Log.final.out", "star/log/cd4_REP1.Log.out", @@ -259,15 +249,18 @@ "star/log/jurkat.Log.progress.out", "star/log/jurkat.SJ.out.tab", "star/samtools_stats", - "star/samtools_stats/cd4_REP1.sorted.bam.flagstat", - "star/samtools_stats/cd4_REP1.sorted.bam.idxstats", - "star/samtools_stats/cd4_REP1.sorted.bam.stats", - "star/samtools_stats/cd4_REP2.sorted.bam.flagstat", - "star/samtools_stats/cd4_REP2.sorted.bam.idxstats", - "star/samtools_stats/cd4_REP2.sorted.bam.stats", - "star/samtools_stats/jurkat.sorted.bam.flagstat", - "star/samtools_stats/jurkat.sorted.bam.idxstats", - "star/samtools_stats/jurkat.sorted.bam.stats", + "star/samtools_stats/cd4_REP1_genome.flagstat", + "star/samtools_stats/cd4_REP1_genome.idxstats", + "star/samtools_stats/cd4_REP1_genome.stats", + "star/samtools_stats/cd4_REP2_genome.flagstat", + "star/samtools_stats/cd4_REP2_genome.idxstats", + "star/samtools_stats/cd4_REP2_genome.stats", + "star/samtools_stats/jurkat_genome.flagstat", + "star/samtools_stats/jurkat_genome.idxstats", + "star/samtools_stats/jurkat_genome.stats", + "star/samtools_stats/jurkat_transcriptome.flagstat", + "star/samtools_stats/jurkat_transcriptome.idxstats", + "star/samtools_stats/jurkat_transcriptome.stats", "star/star", "star/star/Genome", "star/star/Log.out", @@ -351,15 +344,18 @@ "cd4_REP1.SJ.out.tab:md5,991ac1fa28719c078a4827fcf66e90b0", "cd4_REP2.SJ.out.tab:md5,5accd405e613d28731f111dfd070a3ba", "jurkat.SJ.out.tab:md5,8e5de2dc83e2478528528a86a2ffd456", - "cd4_REP1.sorted.bam.flagstat:md5,6379888a79d90e28dd969e21f7b03a33", - "cd4_REP1.sorted.bam.idxstats:md5,65e8e2d1ed65620f9750f2981e997a9d", - "cd4_REP1.sorted.bam.stats:md5,bec325c0cd30bafd9758c0535f99cf49", - "cd4_REP2.sorted.bam.flagstat:md5,ab83e3fbca17cf463fc5293a82e4bb3a", - "cd4_REP2.sorted.bam.idxstats:md5,9cdf3dd50a9862a02592c3768071fe32", - "cd4_REP2.sorted.bam.stats:md5,c7a92c340bb5735414d035da30b9b53f", - "jurkat.sorted.bam.flagstat:md5,b5f1d127de493e406882aced667210c9", - "jurkat.sorted.bam.idxstats:md5,5e4a68fda75c954324d659af58d12c62", - "jurkat.sorted.bam.stats:md5,0b7a4d6e0823d159ab2d9cdc1b2c8310", + "cd4_REP1_genome.flagstat:md5,6379888a79d90e28dd969e21f7b03a33", + "cd4_REP1_genome.idxstats:md5,65e8e2d1ed65620f9750f2981e997a9d", + "cd4_REP1_genome.stats:md5,49ea194b2d955cef24987a32dea3f6bb", + "cd4_REP2_genome.flagstat:md5,ab83e3fbca17cf463fc5293a82e4bb3a", + "cd4_REP2_genome.idxstats:md5,9cdf3dd50a9862a02592c3768071fe32", + "cd4_REP2_genome.stats:md5,f878081edfbda2977e38685d12434c43", + "jurkat_genome.flagstat:md5,b5f1d127de493e406882aced667210c9", + "jurkat_genome.idxstats:md5,5e4a68fda75c954324d659af58d12c62", + "jurkat_genome.stats:md5,5bf21e33fb56e0a38b53faf34b3be2ea", + "jurkat_transcriptome.flagstat:md5,2e10f27f80137c7ca4d340f110aa8fcf", + "jurkat_transcriptome.idxstats:md5,8e38ac91c083ef3c5cf77ba782b836a5", + "jurkat_transcriptome.stats:md5,322d7e620bcce35529aca042d0c8b3e8", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,1c9cd646313f1abb1cfc205ccab73464", @@ -390,7 +386,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-20T20:36:26.671409" + "timestamp": "2024-12-20T21:16:25.416797" }, "gzip_software_versions": { "content": [