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Update subworkflows/nf-core/bam_qc_picard/main.nf

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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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Matthias De Smet 2022-04-29 14:26:06 +02:00 committed by GitHub
parent 343c0ebe20
commit 7e391c3a3b
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subworkflows/nf-core/bam_qc_picard/main.nf
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@ -25,7 +25,7 @@ workflow BAM_QC_PICARD {
if (!ch_bait_interval) log.error("Bait interval channel is empty") if (!ch_bait_interval) log.error("Bait interval channel is empty")
if (!ch_target_interval) log.error("Target interval channel is empty") if (!ch_target_interval) log.error("Target interval channel is empty")
PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval ) PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
ch_coverage_metrics = PICARD_COLLECTHSMETRICS.out.metrics ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
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, ch_fasta ) PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )