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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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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [[#327](https://github.com/nf-core/atacseq/issues/327)]Consistently support `.csi` indices as alternative to `.bai` to allow SAMTOOLS_INDEX to be used with the `-c` flag

## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-08-07

### Enhancements & fixes
Expand Down
17 changes: 15 additions & 2 deletions subworkflows/local/bam_filter_bamtools.nf
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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), [ csi ] ]
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
39 changes: 31 additions & 8 deletions workflows/atacseq.nf
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Expand Up @@ -161,7 +161,6 @@ workflow ATACSEQ {
// SUBWORKFLOW: Alignment with BWA & BAM QC
//
ch_genome_bam = Channel.empty()
ch_genome_bam_index = Channel.empty()
ch_samtools_stats = Channel.empty()
ch_samtools_flagstat = Channel.empty()
ch_samtools_idxstats = Channel.empty()
Expand All @@ -176,7 +175,6 @@ workflow ATACSEQ {
}
)
ch_genome_bam = FASTQ_ALIGN_BWA.out.bam
ch_genome_bam_index = FASTQ_ALIGN_BWA.out.bai
ch_samtools_stats = FASTQ_ALIGN_BWA.out.stats
ch_samtools_flagstat = FASTQ_ALIGN_BWA.out.flagstat
ch_samtools_idxstats = FASTQ_ALIGN_BWA.out.idxstats
Expand All @@ -198,7 +196,6 @@ workflow ATACSEQ {
}
)
ch_genome_bam = FASTQ_ALIGN_BOWTIE2.out.bam
ch_genome_bam_index = FASTQ_ALIGN_BOWTIE2.out.bai
ch_samtools_stats = FASTQ_ALIGN_BOWTIE2.out.stats
ch_samtools_flagstat = FASTQ_ALIGN_BOWTIE2.out.flagstat
ch_samtools_idxstats = FASTQ_ALIGN_BOWTIE2.out.idxstats
Expand All @@ -222,7 +219,6 @@ workflow ATACSEQ {
[]
)
ch_genome_bam = FASTQ_ALIGN_CHROMAP.out.bam
ch_genome_bam_index = FASTQ_ALIGN_CHROMAP.out.bai
ch_samtools_stats = FASTQ_ALIGN_CHROMAP.out.stats
ch_samtools_flagstat = FASTQ_ALIGN_CHROMAP.out.flagstat
ch_samtools_idxstats = FASTQ_ALIGN_CHROMAP.out.idxstats
Expand All @@ -244,7 +240,6 @@ workflow ATACSEQ {
params.seq_center ?: ''
)
ch_genome_bam = ALIGN_STAR.out.bam
ch_genome_bam_index = ALIGN_STAR.out.bai
ch_samtools_stats = ALIGN_STAR.out.stats
ch_samtools_flagstat = ALIGN_STAR.out.flagstat
ch_samtools_idxstats = ALIGN_STAR.out.idxstats
Expand Down Expand Up @@ -298,7 +293,17 @@ workflow ATACSEQ {
// SUBWORKFLOW: Filter BAM file
//
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 +384,16 @@ 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 +491,16 @@ 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
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