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Actually add the changes

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This commit is contained in:
James Fellows Yates 2022-05-31 15:49:57 +02:00
parent edc9e83a7d
commit 089f761f0b
1 changed files with 3 additions and 2 deletions
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5
modules/filtlong/main.nf
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@ -11,7 +11,7 @@ process FILTLONG {
tuple val(meta), path(shortreads), path(longreads) tuple val(meta), path(shortreads), path(longreads)
output: output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -21,12 +21,13 @@ process FILTLONG {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
""" """
filtlong \\ filtlong \\
$short_reads \\ $short_reads \\
$args \\ $args \\
$longreads \\ $longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz | gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":