def VERSION = '1.5.0' // Version information not provided by tool on CLI process GTDBTK_CLASSIFYWF { tag "${meta.assembler}-${meta.id}" conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : 'quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0' }" input: tuple val(meta), path("bins/*") tuple val(db_name), path("database/*") output: path "gtdbtk.${meta.assembler}-${meta.id}.*.summary.tsv" , emit: summary path "gtdbtk.${meta.assembler}-${meta.id}.*.classify.tree.gz" , emit: tree path "gtdbtk.${meta.assembler}-${meta.id}.*.markers_summary.tsv", emit: markers path "gtdbtk.${meta.assembler}-${meta.id}.*.msa.fasta.gz" , emit: msa path "gtdbtk.${meta.assembler}-${meta.id}.*.user_msa.fasta" , emit: user_msa path "gtdbtk.${meta.assembler}-${meta.id}.*.filtered.tsv" , emit: filtered path "gtdbtk.${meta.assembler}-${meta.id}.log" , emit: log path "gtdbtk.${meta.assembler}-${meta.id}.warnings.log" , emit: warnings path "gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv" , emit: failed path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : "" """ export GTDBTK_DATA_PATH="\${PWD}/database" if [ ${pplacer_scratch} != "" ] ; then mkdir pplacer_tmp fi gtdbtk classify_wf \\ $args \\ --genome_dir bins \\ --prefix "gtdbtk.${meta.assembler}-${meta.id}" \\ --out_dir "\${PWD}" \\ --cpus $task.cpus \\ --pplacer_cpus $params.gtdbtk_pplacer_cpus \\ $pplacer_scratch \\ --min_perc_aa $params.gtdbtk_min_perc_aa \\ --min_af $params.gtdbtk_min_af gzip "gtdbtk.${meta.assembler}-${meta.id}".*.classify.tree "gtdbtk.${meta.assembler}-${meta.id}".*.msa.fasta mv gtdbtk.log "gtdbtk.${meta.assembler}-${meta.id}.log" mv gtdbtk.warnings.log "gtdbtk.${meta.assembler}-${meta.id}.warnings.log" cat <<-END_VERSIONS > versions.yml "${task.process}": gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//") END_VERSIONS """ stub: """ touch gtdbtk.${meta.assembler}-${meta.id}.stub.summary.tsv touch gtdbtk.${meta.assembler}-${meta.id}.stub.classify.tree.gz touch gtdbtk.${meta.assembler}-${meta.id}.stub.markers_summary.tsv touch gtdbtk.${meta.assembler}-${meta.id}.stub.msa.fasta.gz touch gtdbtk.${meta.assembler}-${meta.id}.stub.user_msa.fasta touch gtdbtk.${meta.assembler}-${meta.id}.stub.filtered.tsv touch gtdbtk.${meta.assembler}-${meta.id}.log touch gtdbtk.${meta.assembler}-${meta.id}.warnings.log touch gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": gtdbtk: $VERSION END_VERSIONS """ }