process LAST_LASTAL { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : 'quay.io/biocontainers/last:1250--h2e03b76_0' }" input: tuple val(meta), path(fastx), path (param_file) path index output: tuple val(meta), path("*.maf.gz"), emit: maf path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def trained_params = param_file ? "-p ${param_file}" : '' """ INDEX_NAME=\$(basename \$(ls $index/*.des) .des) lastal \\ $trained_params \\ $args \\ -P $task.cpus \\ ${index}/\$INDEX_NAME \\ $fastx \\ | gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz # gzip needs --no-name otherwise it puts a timestamp in the file, # which makes its checksum non-reproducible. cat <<-END_VERSIONS > versions.yml "${task.process}": last: \$(lastal --version 2>&1 | sed 's/lastal //') END_VERSIONS """ }