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Fix bam filtering #1080

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merged 4 commits into from
Jul 25, 2024
Merged

Fix bam filtering #1080

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a2fff87
support csi indexes
TCLamnidis Jul 25, 2024
e2db18f
dummy commit to restart github actions
TCLamnidis Jul 25, 2024
2fe53bd
Revert "dummy commit to restart github actions"
TCLamnidis Jul 25, 2024
7765f16
pick up csi indices for SAMTOOLS_FLAGSTATS_BAM_INPUT
TCLamnidis Jul 25, 2024
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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -578,8 +578,8 @@ process {
}

withName: ".*BAM_SPLIT_BY_REGION:SAMTOOLS_INDEX" {
// The BAM_SPLIT_BY_REGION SWF only works with bais, so `params.fasta_largeref` should not be passed to it.
tag = { "${meta.reference}:${meta.genomic_region}|${meta.sample_id}_${meta.library_id}" }
ext.args = { params.fasta_largeref ? "-c" : "" }
ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}_${meta.genomic_region}_dedupped" }
publishDir = [
enabled: false
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8 changes: 5 additions & 3 deletions subworkflows/local/bamfiltering.nf
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Expand Up @@ -16,7 +16,7 @@ include { CAT_FASTQ as CAT_FASTQ_MAPPED } from '../../modules/
workflow FILTER_BAM {

take:
bam // [ [meta], [bam], [bai] ]
bam // [ [meta], [bam], [bai/csi] ]

main:
ch_versions = Channel.empty()
Expand All @@ -37,9 +37,10 @@ workflow FILTER_BAM {
ch_versions = ch_versions.mix( FILTER_BAM_FRAGMENT_LENGTH.out.versions.first() )

SAMTOOLS_LENGTH_FILTER_INDEX ( FILTER_BAM_FRAGMENT_LENGTH.out.bam )
ch_length_filtered_index = params.fasta_largeref ? SAMTOOLS_LENGTH_FILTER_INDEX.out.csi : SAMTOOLS_LENGTH_FILTER_INDEX.out.bai
ch_versions = ch_versions.mix( SAMTOOLS_LENGTH_FILTER_INDEX.out.versions.first() )

ch_bam_for_qualityfilter = FILTER_BAM_FRAGMENT_LENGTH.out.bam.join( SAMTOOLS_LENGTH_FILTER_INDEX.out.bai )
ch_bam_for_qualityfilter = FILTER_BAM_FRAGMENT_LENGTH.out.bam.join( ch_length_filtered_index )

} else {
ch_bam_for_qualityfilter = bam
Expand All @@ -52,9 +53,10 @@ workflow FILTER_BAM {
ch_versions = ch_versions.mix( SAMTOOLS_VIEW_BAM_FILTERING.out.versions.first() )

SAMTOOLS_FILTER_INDEX ( SAMTOOLS_VIEW_BAM_FILTERING.out.bam )
ch_filtered_bam_index = params.fasta_largeref ? SAMTOOLS_FILTER_INDEX.out.csi : SAMTOOLS_FILTER_INDEX.out.bai
ch_versions = ch_versions.mix( SAMTOOLS_FILTER_INDEX.out.versions.first() )

ch_bam_for_genomics = SAMTOOLS_VIEW_BAM_FILTERING.out.bam.join( SAMTOOLS_FILTER_INDEX.out.bai )
ch_bam_for_genomics = SAMTOOLS_VIEW_BAM_FILTERING.out.bam.join( ch_filtered_bam_index )

// Only run if we actually remove mapped reads
if ( params.bamfiltering_mappingquality != 0 || params.bamfiltering_minreadlength != 0 ) {
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5 changes: 1 addition & 4 deletions workflows/eager.nf
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Expand Up @@ -207,10 +207,7 @@ workflow EAGER {
//
// MODULE: flagstats of user supplied input BAMs
//
ch_bam_bai_input = ch_samplesheet_bams
.join(SAMTOOLS_INDEX_BAM_INPUT.out.bai)

SAMTOOLS_FLAGSTATS_BAM_INPUT ( ch_bam_bai_input )
SAMTOOLS_FLAGSTATS_BAM_INPUT ( ch_bams_from_input )
ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTATS_BAM_INPUT.out.versions )
ch_flagstat_input_bam = SAMTOOLS_FLAGSTATS_BAM_INPUT.out.flagstat // For endorspy

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