nf-core_modules/modules/svdb/query/main.nf
Ramprasad Neethiraj 5297d27fbf
update svdb to version 2.5.2 (#1390)
* update svdb version and tests

* update link
2022-03-21 10:39:34 +01:00

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1.8 KiB
Text

process SVDB_QUERY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
input:
tuple val(meta), path(vcf)
val(in_occs)
val(in_frqs)
val(out_occs)
val(out_frqs)
path (vcf_dbs)
output:
tuple val(meta), path("*_query.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 in_occ = ""
def in_frq = ""
def out_occ = ""
def out_frq = ""
if (in_occs) {
in_occ = "--in_occ ${in_occs.join(',')}"
}
if (in_frqs) {
in_frq = "--in_frq ${in_frqs.join(',')}"
}
if (out_occs) {
out_occ = "--out_occ ${out_occs.join(',')}"
}
if (out_frqs) {
out_frq = "--out_frq ${out_frqs.join(',')}"
}
"""
svdb \\
--query \\
$in_occ \\
$in_frq \\
$out_occ \\
$out_frq \\
$args \\
--db ${vcf_dbs.join(',')} \\
--query_vcf $vcf \\
--prefix ${prefix}
cat <<-END_VERSIONS > versions.yml
"${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 ${prefix}_query.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS
"""
}