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72 lines
2.8 KiB
Text
72 lines
2.8 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(fasta) // Required: meta map, and fasta sequence file
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each lineage // Required: lineage to check against
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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"), 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_dir = busco_lineages_path ? "--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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# . "/usr/local/env-activate.sh" # Errors out because of various unbound variables
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export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
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export CONDA_PREFIX='/usr/local'
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export CONDA_SHLVL='1'
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export CONDA_DEFAULT_ENV='/usr/local'
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export CONDA_PROMPT_MODIFIER=''
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. "/usr/local/etc/conda/activate.d/activate-r-base.sh"
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. "/usr/local/etc/conda/activate.d/augustus.sh"
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. "/usr/local/etc/conda/activate.d/openjdk_activate.sh"
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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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gzip -cdf $fasta > ${prefix}_uncompressed.fasta
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busco \\
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--cpu $task.cpus \\
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--in ${prefix}_uncompressed.fasta \\
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--out ${prefix}-busco \\
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--lineage_dataset $lineage \\
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$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 ${prefix}_uncompressed.fasta
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cat <<-END_VERSIONS > versions.yml
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"${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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