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fix outputs

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This commit is contained in:
Matthias De Smet 2022-04-28 13:42:14 +02:00
parent dee8ec9e91
commit e0a8af8693
2 changed files with 10 additions and 12 deletions
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14
subworkflows/nf-core/bam_qc_picard/main.nf
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@ -8,7 +8,7 @@ include { PICARD_COLLECTHSMETRICS } from '../../../modules/picard/collecth
workflow BAM_QC_PICARD { workflow BAM_QC_PICARD {
take: take:
ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ] ch_bam // channel: [ val(meta), [ bam ]]
ch_fasta // channel: [ fasta ] ch_fasta // channel: [ fasta ]
ch_bait_interval // channel: [ bait_interval ] ch_bait_interval // channel: [ bait_interval ]
ch_target_interval // channel: [ target_interval ] ch_target_interval // channel: [ target_interval ]
@ -16,7 +16,7 @@ workflow BAM_QC_PICARD {
main: main:
ch_versions = Channel.empty() ch_versions = Channel.empty()
PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta ) PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
if (ch_bait_interval || ch_target_interval) { if (ch_bait_interval || ch_target_interval) {
if (ch_bait_interval.isEmpty()) { if (ch_bait_interval.isEmpty()) {
@ -25,16 +25,18 @@ workflow BAM_QC_PICARD {
if (ch_target_interval.isEmpty()) { if (ch_target_interval.isEmpty()) {
log.error("Target interval channel is empty") log.error("Target interval channel is empty")
} }
PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval ) PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_bait_interval, ch_target_interval )
ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
} else { } else {
PICARD_COLLECTWGSMETRICS( ch_bam_bai, ch_fasta ) PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
} }
ch_coverage_metrics = Channel.empty()
ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first(), PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
emit: emit:
hs_metrics = PICARD_COLLECTHSMETRICS.out.hs_metrics // channel: [ val(meta), [ hs_metrics ] ] coverage_metrics = PICARD_COLLECTWGSMETRICS.out.metrics // channel: [ val(meta), [ coverage_metrics ] ]
wgs_metrics = PICARD_COLLECTWGSMETRICS.out.metrics // channel: [ val(meta), [ wgs_metrics ] ]
multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ] multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
versions = ch_versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]

8
subworkflows/nf-core/bam_qc_picard/meta.yml
View file

@ -44,14 +44,10 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- hs_metrics: - coverage_metrics:
type: file type: file
description: Alignment metrics files generated by picard CollectHsMetrics description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
pattern: "*_metrics.txt" pattern: "*_metrics.txt"
- wgs_metrics:
type: file
description: Alignment metrics files generated by picard CollectWgsMetrics
pattern: "*_{metrics}"
- multiple_metrics: - multiple_metrics:
type: file type: file
description: Alignment metrics files generated by picard CollectMultipleMetrics description: Alignment metrics files generated by picard CollectMultipleMetrics