nf-core_modules/modules/svdb/merge/main.nf
Ramprasad Neethiraj f44e6c74b4
Add svdb/merge (#1233)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* add stub

* add when
2022-02-04 15:29:44 +01:00

52 lines
1.5 KiB
Text

process SVDB_MERGE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
input:
tuple val(meta), path(vcfs)
val (priority)
output:
tuple val(meta), path("*_sv_merge.vcf"), emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input = ""
for (int index = 0; index < vcfs.size(); index++) {
input += " ${vcfs[index]}:${priority[index]}"
}
"""
svdb \\
--merge \\
$args \\
--priority ${priority.join(',')} \\
--vcf $input \\
> ${prefix}_sv_merge.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_sv_merge.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS
"""
}