process PANGOLIN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : 'quay.io/biocontainers/pangolin:4.1.1--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path('*.csv'), emit: report 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}" """ 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 """ }