nf-core_modules/modules/ffq/main.nf

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2022-07-01 06:59:13 +00:00
process FFQ {
tag "${ids.size() == 1 ? ids[0] : "${ids[0]+'..'+ids[-1]}"}"
label 'process_low'
conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0':
'quay.io/biocontainers/ffq:0.2.1--pyhdfd78af_0' }"
input:
val ids
output:
path "*.json" , emit: json
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def id_list = ids.sort()
def name = id_list.size() == 1 ? ids[0] : 'metadata'
def prefix = task.ext.prefix ?: "${name}"
"""
ffq \\
${id_list.join(' ')} \\
$args \\
> ${prefix}.json
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ffq: \$(echo \$(ffq --help 2>&1) | sed 's/^.*ffq //; s/: A command.*\$//' )
END_VERSIONS
"""
}