mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +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
36 lines
1.1 KiB
Text
36 lines
1.1 KiB
Text
process MINIA {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::minia=3.2.6" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
|
|
'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path('*.contigs.fa'), emit: contigs
|
|
tuple val(meta), path('*.unitigs.fa'), emit: unitigs
|
|
tuple val(meta), path('*.h5') , emit: h5
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def read_list = reads.join(",")
|
|
"""
|
|
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
|
|
minia \\
|
|
$args \\
|
|
-nb-cores $task.cpus \\
|
|
-in input_files.txt \\
|
|
-out $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
|
|
END_VERSIONS
|
|
"""
|
|
}
|