diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf index 9ebb2805..4392c700 100644 --- a/modules/lofreq/callparallel/main.nf +++ b/modules/lofreq/callparallel/main.nf @@ -20,12 +20,12 @@ 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 - path "*.version.txt" , emit: version + tuple val(meta), path("*.vcf.gz"), emit: vcf + path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) @@ -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 """ } diff --git a/modules/lofreq/callparallel/meta.yml b/modules/lofreq/callparallel/meta.yml index 43756e2b..3154f412 100644 --- a/modules/lofreq/callparallel/meta.yml +++ b/modules/lofreq/callparallel/meta.yml @@ -51,3 +51,4 @@ output: authors: - "@kaurravneet4123" + - "@bjohnnyd" diff --git a/tests/modules/lofreq/callparallel/test.yml b/tests/modules/lofreq/callparallel/test.yml index 3ffb459e..e09f68c3 100644 --- a/tests/modules/lofreq/callparallel/test.yml +++ b/tests/modules/lofreq/callparallel/test.yml @@ -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=']