Skip to content

Commit

Permalink
test: That's why STAR is outputting samtools
Browse files Browse the repository at this point in the history
  • Loading branch information
@edmundmiller
edmundmiller committed Dec 21, 2024
1 parent 6329b2c commit d51a450
Show file tree
Hide file tree
Showing 3 changed files with 46 additions and 33 deletions.
23 changes: 21 additions & 2 deletions conf/modules.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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" },
Expand All @@ -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}" },
Expand All @@ -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 = { [
Expand Down
2 changes: 0 additions & 2 deletions tests/.nftignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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}
Expand Down
54 changes: 25 additions & 29 deletions workflows/tests/aligner/star.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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": [
Expand Down

0 comments on commit d51a450

Please sign in to comment.