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Merge pull request #1713 from jfy133/fix-filtlong

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Fix filtlong to remove hardcoded output names
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James A. Fellows Yates 2022-05-31 20:50:21 +02:00 committed by GitHub
commit 33af85697b
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3 changed files with 7 additions and 5 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}":

1
tests/modules/filtlong/nextflow.config
View file

@ -3,5 +3,6 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = "--min_length 10" ext.args = "--min_length 10"
ext.prefix = "test_lr"
} }

6
tests/modules/filtlong/test.yml
View file

@ -3,7 +3,7 @@
tags: tags:
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr_filtlong.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
@ -12,7 +12,7 @@
tags: tags:
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr_filtlong.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
@ -21,6 +21,6 @@
tags: tags:
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr_filtlong.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"