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fix: lofreq/callparallel missing arg (#562) (#586)

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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Johnathan D 2021-07-19 09:19:27 +01:00 committed by GitHub
parent 8c294882d7
commit 0b40798d1b
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3 changed files with 13 additions and 10 deletions
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11
modules/lofreq/callparallel/main.nf
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@ -20,11 +20,11 @@ process LOFREQ_CALLPARALLEL {
input:
tuple val(meta), path(bam), path(bai)
file fasta
file fai
path fasta
path fai
output:
tuple val(meta), path("*.vcf"), emit: vcf
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "*.version.txt" , emit: version
script:
@ -34,10 +34,11 @@ process LOFREQ_CALLPARALLEL {
lofreq \\
call-parallel \\
--pp-threads $task.cpus \\
$options.args \\
-f $fasta \\
-o ${prefix}.vcf \\
-o ${prefix}.vcf.gz \\
$bam
echo \$(lofreq version 2>&1) | sed 's/^.*lofreq //; s/Using.*\$//' > ${software}.version.txt
echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt
"""
}

1
modules/lofreq/callparallel/meta.yml
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@ -51,3 +51,4 @@ output:
authors:
- "@kaurravneet4123"
- "@bjohnnyd"

9
tests/modules/lofreq/callparallel/test.yml
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@ -1,7 +1,8 @@
- name: lofreq callparallel
command: nextflow run ./tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c tests/config/nextflow.config
- name: lofreq callparallel test_lofreq_callparallel
command: nextflow run tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c tests/config/nextflow.config
tags:
- lofreq
- lofreq/callparallel
- lofreq
files:
- path: output/lofreq/test.vcf
- path: output/lofreq/test.vcf.gz
contains: ['##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">']