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taxprofiler/modules/nf-core/eido/convert/main.nf

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process EIDO_CONVERT {
tag "$samplesheet"
label 'process_single'
conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
'biocontainers/eido:0.1.9_cv1' }"
input:
path samplesheet
val format
path pep_input_base_dir
output:
path "versions.yml" , emit: versions
path "${prefix}.${format}" , emit: samplesheet_converted
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "samplesheet_converted"
"""
eido \\
convert \\
-f $format \\
$samplesheet \\
$args \\
-p samples=${prefix}.${format}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
END_VERSIONS
"""
}