process BUSCO { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.3.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0': 'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }" input: tuple val(meta), path('tmp_input/*') each lineage // Required: lineage to check against, "auto" enables --auto-lineage instead path busco_lineages_path // Recommended: path to busco lineages - downloads if not set path config_file // Optional: busco configuration file output: tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt, optional: true tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true tuple val(meta), path("*-busco") , emit: busco_dir path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}-${lineage}" def busco_config = config_file ? "--config $config_file" : '' def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}" def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : '' """ # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) # Check for container variable initialisation script and source it. if [ -f "/usr/local/env-activate.sh" ]; then set +u # Otherwise, errors out because of various unbound variables . "/usr/local/env-activate.sh" set -u fi # If the augustus config directory is not writable, then copy to writeable area if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then # Create writable tmp directory for augustus AUG_CONF_DIR=\$( mktemp -d -p \$PWD ) cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}" fi # Ensure the input is uncompressed INPUT_SEQS=input_seqs mkdir "\$INPUT_SEQS" cd "\$INPUT_SEQS" for FASTA in ../tmp_input/*; do if [ "\${FASTA##*.}" == 'gz' ]; then gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz ) else ln -s "\$FASTA" . fi done cd .. busco \\ --cpu $task.cpus \\ --in "\$INPUT_SEQS" \\ --out ${prefix}-busco \\ $busco_lineage \\ $busco_lineage_dir \\ $busco_config \\ $args # clean up rm -rf "\$INPUT_SEQS" # Move files to avoid staging/publishing issues mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found." cat <<-END_VERSIONS > versions.yml "${task.process}": busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' ) END_VERSIONS """ }