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Add consistent support of .csi indices as alternative to .bai #328

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merged 5 commits into from
Aug 11, 2023
Merged

Add consistent support of .csi indices as alternative to .bai #328

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b4a8983
Add consistent support of .csi indices as alternative to .bai
Aug 10, 2023
7ab1cd9
Changes from code review
Aug 11, 2023
5117171
Make Prettier happy
Aug 11, 2023
947dde3
Remove unused code
Aug 11, 2023
79284fb
Update CHANGELOG.md
bjlang Aug 11, 2023
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17 changes: 15 additions & 2 deletions subworkflows/local/bam_filter_bamtools.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ workflow BAM_FILTER_BAMTOOLS {
BAMTOOLS_FILTER
.out
.bam
.branch {
.branch {
meta, bam ->
single_end: meta.single_end
return [ meta, bam ]
Expand All @@ -49,11 +49,23 @@ workflow BAM_FILTER_BAMTOOLS {
}
ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())

SAMTOOLS_INDEX.out.bai
.join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true)
.map {
meta, bai, csi ->
if (bai) {
[ meta, bai ]
} else {
[ meta, csi ]
}
}
.set { ch_index }

//
// Run samtools stats, flagstat and idxstats on SE BAM
//
BAM_STATS_SAMTOOLS (
ch_bam.single_end.join(SAMTOOLS_INDEX.out.bai),
ch_bam.single_end.join(ch_index),
ch_fasta
)
ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first())
Expand Down Expand Up @@ -87,6 +99,7 @@ workflow BAM_FILTER_BAMTOOLS {
name_bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ]
bam = BAM_SORT_STATS_SAMTOOLS.out.bam.mix(ch_bam.single_end) // channel: [ val(meta), [ bam ] ]
bai = BAM_SORT_STATS_SAMTOOLS.out.bai.mix(SAMTOOLS_INDEX.out.bai) // channel: [ val(meta), [ bai ] ]
csi = BAM_SORT_STATS_SAMTOOLS.out.csi.mix(SAMTOOLS_INDEX.out.csi) // channel: [ val(meta), [ bai ] ]
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stats = BAM_SORT_STATS_SAMTOOLS.out.stats.mix(BAM_STATS_SAMTOOLS.out.stats) // channel: [ val(meta), [ stats ] ]
flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat.mix(BAM_STATS_SAMTOOLS.out.flagstat) // channel: [ val(meta), [ flagstat ] ]
idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats.mix(BAM_STATS_SAMTOOLS.out.idxstats) // channel: [ val(meta), [ idxstats ] ]
Expand Down
45 changes: 42 additions & 3 deletions workflows/atacseq.nf
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Expand Up @@ -297,8 +297,29 @@ workflow ATACSEQ {
//
// SUBWORKFLOW: Filter BAM file
//
// ch_bam_bai = PICARD_MARKDUPLICATES.out.bam
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// .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
// .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true)
// .map {
// meta, bam, bai, csi ->
// if (bai) {
// [ meta, bam, bai ]
// } else {
// [ meta, bam, csi ]
// }
// }
MERGED_LIBRARY_FILTER_BAM (
MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bam.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bai, by: [0]),
MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bam
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bai, by: [0], remainder: true)
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.csi, by: [0], remainder: true)
.map {
meta, bam, bai, csi ->
if (bai) {
[ meta, bam, bai ]
} else {
[ meta, bam, csi ]
}
},
PREPARE_GENOME.out.filtered_bed.first(),
PREPARE_GENOME
.out
Expand Down Expand Up @@ -379,7 +400,16 @@ workflow ATACSEQ {
MERGED_LIBRARY_FILTER_BAM
.out
.bam
.join(MERGED_LIBRARY_FILTER_BAM.out.bai, by: [0])
.join(MERGED_LIBRARY_FILTER_BAM.out.bai, by: [0], remainder: true)
.join(MERGED_LIBRARY_FILTER_BAM.out.csi, by: [0], remainder: true)
.map {
meta, bam, bai, csi ->
if (bai) {
[ meta, bam, bai ]
} else {
[ meta, bam, csi ]
}
}
.set { ch_bam_bai }

if (params.with_control) {
Expand Down Expand Up @@ -477,7 +507,16 @@ workflow ATACSEQ {
MERGED_LIBRARY_MARKDUPLICATES_PICARD
.out
.bam
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bai, by: [0])
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.bai, by: [0], remainder: true)
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.csi, by: [0], remainder: true)
.map {
meta, bam, bai, csi ->
if (bai) {
[ meta, bam, bai ]
} else {
[ meta, bam, csi ]
}
}
.join(MERGED_LIBRARY_CALL_ANNOTATE_PEAKS.out.peaks, by: [0])
.set { ch_bam_peaks }

Expand Down