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update command line syntax for all tools

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This commit is contained in:
Matthias De Smet 2022-04-29 07:57:11 +02:00
parent 6ca6de91f8
commit 00467ac64a
7 changed files with 21 additions and 21 deletions
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2
modules/picard/addorreplacereadgroups/main.nf
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@ -43,7 +43,7 @@ process PICARD_ADDORREPLACEREADGROUPS {
-PL ${PLATFORM} \\ -PL ${PLATFORM} \\
-PU ${BARCODE} \\ -PU ${BARCODE} \\
-SM ${SAMPLE} \\ -SM ${SAMPLE} \\
-CREATE_INDEX true --CREATE_INDEX true
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

8
modules/picard/collecthsmetrics/main.nf
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@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
CollectHsMetrics \\ CollectHsMetrics \\
$args \\ $args \\
$reference \\ $reference \\
-BAIT_INTERVALS $bait_intervals \\ --BAIT_INTERVALS $bait_intervals \\
-TARGET_INTERVALS $target_intervals \\ --TARGET_INTERVALS $target_intervals \\
-INPUT $bam \\ --INPUT $bam \\
-OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

6
modules/picard/collectmultiplemetrics/main.nf
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@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CollectMultipleMetrics \\ CollectMultipleMetrics \\
$args \\ $args \\
INPUT=$bam \\ --INPUT $bam \\
OUTPUT=${prefix}.CollectMultipleMetrics \\ --OUTPUT ${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

6
modules/picard/collectwgsmetrics/main.nf
View file

@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CollectWgsMetrics \\ CollectWgsMetrics \\
$args \\ $args \\
INPUT=$bam \\ --INPUT $bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

4
modules/picard/createsequencedictionary/main.nf
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@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CreateSequenceDictionary \\ CreateSequenceDictionary \\
$args \\ $args \\
R=$fasta \\ -R $fasta \\
O=${prefix}.dict -O ${prefix}.dict
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

10
modules/picard/liftovervcf/main.nf
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@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
LiftoverVcf \\ LiftoverVcf \\
$args \\ $args \\
I=$input_vcf \\ -I $input_vcf \\
O=${prefix}.lifted.vcf.gz \\ -O ${prefix}.lifted.vcf.gz \\
CHAIN=$chain \\ --CHAIN $chain \\
REJECT=${prefix}.unlifted.vcf.gz \\ --REJECT ${prefix}.unlifted.vcf.gz \\
R=$fasta -R $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

6
modules/picard/markduplicates/main.nf
View file

@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
MarkDuplicates \\ MarkDuplicates \\
$args \\ $args \\
I=$bam \\ -I $bam \\
O=${prefix}.bam \\ -O ${prefix}.bam \\
M=${prefix}.MarkDuplicates.metrics.txt -M ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":