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