process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.53" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' : 'quay.io/biocontainers/malt:0.53--hdfd78af_0' }" input: path fastas val seq_type path gff path map_db output: path "malt_index/" , emit: index path "versions.yml" , emit: versions path "malt-build.log", emit: log when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def avail_mem = 6 if (!task.memory) { log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } def igff = gff ? "-igff ${gff}" : "" """ malt-build \\ -J-Xmx${avail_mem}g \\ -v \\ --input ${fastas.join(' ')} \\ -s $seq_type \\ $igff \\ -d 'malt_index/' \\ -t $task.cpus \\ $args \\ -mdb ${map_db}/*.db |&tee malt-build.log cat <<-END_VERSIONS > versions.yml "${task.process}": malt: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2) END_VERSIONS """ }