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Fixed an issue with wrong file order

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 09:07:52 +02:00
parent 7956d38e61
commit 85c49a971f
1 changed files with 6 additions and 3 deletions
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9
modules/vardictjava/main.nf
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@ -8,9 +8,8 @@ process VARDICTJAVA {
'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(regions_of_interest)
path(reference_fasta) path(reference_fasta)
path(regions_of_interest)
output: output:
tuple val(meta), path("*.vcf"), emit: vcf tuple val(meta), path("*.vcf"), emit: vcf
@ -24,6 +23,9 @@ process VARDICTJAVA {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
head -n 20 $reference_fasta
cat $reference_fasta | wc -l
vardict-java \\ vardict-java \\
$args \\ $args \\
-b $bam \\ -b $bam \\
@ -31,10 +33,11 @@ process VARDICTJAVA {
-n $prefix \\ -n $prefix \\
-G $reference_fasta \\ -G $reference_fasta \\
$regions_of_interest \\ $regions_of_interest \\
> ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
vardictjava: \$(echo 1.8.3) vardict-java: \$(echo 1.8.3)
END_VERSIONS END_VERSIONS
""" """
} }