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https://github.com/MillironX/nf-core_modules.git
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54 lines
2.2 KiB
Text
54 lines
2.2 KiB
Text
process BUSCO {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::busco=5.2.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0':
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'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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val(mode)
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path(augustus_config)
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val(lineage)
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output:
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tuple val(meta), path("${meta.id}/run_*/full_table.tsv"), emit: tsv
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tuple val(meta), path("${meta.id}/run_*/short_summary.txt"), emit: txt
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path "versions.yml" , emit: versions
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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}"
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if (lineage) args += " --lineage_dataset $lineage"
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"""
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# Ensure the input is uncompressed
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gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
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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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# Copy the image's AUGUSTUS config directory if it was not provided to the module
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[ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
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# Busco command
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AUGUSTUS_CONFIG_PATH=augustus_config busco $args --augustus --mode $mode --cpu $task.cpus --in __UNCOMPRESSED_FASTA_FILE__ --out $meta.id
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cat <<-END_VERSIONS > versions.yml
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"${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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