mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process ENTREZDIRECT_ESUMMARY {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1':
|
|
'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }"
|
|
|
|
input:
|
|
tuple val(meta), val(uid), path(uids_file)
|
|
val database
|
|
|
|
output:
|
|
tuple val(meta), path("*.xml"), emit: xml
|
|
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}"
|
|
input = uids_file ? "-input ${uids_file}" : "-id ${uid}"
|
|
if (!uid && !uids_file) error "No input. Valid input: an identifier or a .txt file with identifiers"
|
|
if (uid && uids_file) error "Only one input is required: a single identifier or a .txt file with identifiers"
|
|
"""
|
|
esummary \\
|
|
$args \\
|
|
-db $database \\
|
|
$input > ${prefix}.xml
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
esummary: \$(esummary -version)
|
|
END_VERSIONS
|
|
"""
|
|
}
|