mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
32 lines
935 B
Text
32 lines
935 B
Text
process PANGOLIN {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
|
|
'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path('*.csv'), emit: report
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
pangolin \\
|
|
$fasta\\
|
|
--outfile ${prefix}.pangolin.csv \\
|
|
--threads $task.cpus \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
pangolin: \$(pangolin --version | sed "s/pangolin //g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|