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SVDB_MERGE bgzip (#1910)

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* Started (again) to work on bgzipping SVDB_MERGE output

* Updated test yml

* SVDB_MERGE now bgzips output

* Fixed singularity, renamed tests in test.yml

Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
This commit is contained in:
WackerO 2022-07-20 10:54:06 +02:00 committed by GitHub
parent f91abed951
commit 8214b73700
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3 changed files with 10 additions and 10 deletions
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10
modules/svdb/merge/main.nf
View file

@ -1,18 +1,17 @@
process SVDB_MERGE { process SVDB_MERGE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null)
conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0':
'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }" 'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0' }"
input: input:
tuple val(meta), path(vcfs) tuple val(meta), path(vcfs)
val (priority) val (priority)
output: output:
tuple val(meta), path("*_sv_merge.vcf"), emit: vcf tuple val(meta), path("*_sv_merge.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -37,6 +36,7 @@ process SVDB_MERGE {
$prio \\ $prio \\
--vcf $input \\ --vcf $input \\
> ${prefix}_sv_merge.vcf > ${prefix}_sv_merge.vcf
bgzip ${prefix}_sv_merge.vcf
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

2
modules/svdb/merge/meta.yml
View file

@ -34,6 +34,6 @@ output:
- vcf: - vcf:
type: file type: file
description: merged VCF file description: merged VCF file
pattern: "*_sv_merge.vcf" pattern: "*_sv_merge.vcf.gz"
authors: authors:
- "@ramprasadn" - "@ramprasadn"

8
tests/modules/svdb/merge/test.yml
View file

@ -1,14 +1,14 @@
- name: svdb merge - name: svdb merge test_svdb_merge
command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
tags: tags:
- svdb - svdb
- svdb/merge - svdb/merge
files: files:
- path: output/svdb/test_sv_merge.vcf - path: output/svdb/test_sv_merge.vcf.gz
- name: svdb merge noprio - name: svdb merge test_svdb_merge_noprio
command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
tags: tags:
- svdb - svdb
- svdb/merge - svdb/merge
files: files:
- path: output/svdb/test_sv_merge.vcf - path: output/svdb/test_sv_merge.vcf.gz