process HMMER_HMMALIGN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" input: tuple val(meta), path(fasta) path hmm output: tuple val(meta), path("*.sthlm.gz"), emit: sthlm 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}" """ hmmalign \\ $args \\ $hmm \\ $fasta | gzip -c > ${meta.id}.sthlm.gz cat <<-END_VERSIONS > versions.yml "${task.process}": hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//') END_VERSIONS """ }