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picard: make reference sequence optional

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This commit is contained in:
Matthias De Smet 2022-05-21 08:33:49 +02:00
parent c8ccfe3710
commit a5a6973fcf
3 changed files with 5 additions and 3 deletions
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2
modules/picard/collecthsmetrics/main.nf
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@ -24,7 +24,7 @@ process PICARD_COLLECTHSMETRICS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "-R $fasta" : ""
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
def avail_mem = 3
if (!task.memory) {

3
modules/picard/collectmultiplemetrics/main.nf
View file

@ -22,6 +22,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -35,7 +36,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
$args \\
--INPUT $bam \\
--OUTPUT ${prefix}.CollectMultipleMetrics \\
--REFERENCE_SEQUENCE $fasta
$reference
cat <<-END_VERSIONS > versions.yml
"${task.process}":

3
modules/picard/collectwgsmetrics/main.nf
View file

@ -21,6 +21,7 @@ process PICARD_COLLECTWGSMETRICS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -34,7 +35,7 @@ process PICARD_COLLECTWGSMETRICS {
$args \\
--INPUT $bam \\
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
--REFERENCE_SEQUENCE $fasta
$reference
cat <<-END_VERSIONS > versions.yml