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revert wgsmetrics'

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This commit is contained in:
Matthias De Smet 2022-05-22 06:44:05 +02:00
parent 4da143ce62
commit c390385cf5
1 changed files with 1 additions and 2 deletions
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3
modules/picard/collectwgsmetrics/main.nf
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@ -21,7 +21,6 @@ process PICARD_COLLECTWGSMETRICS {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
def avail_mem = 3 def avail_mem = 3
if (!task.memory) { if (!task.memory) {
log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -35,7 +34,7 @@ process PICARD_COLLECTWGSMETRICS {
$args \\ $args \\
--INPUT $bam \\ --INPUT $bam \\
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
$reference --REFERENCE_SEQUENCE ${fasta}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml