Busco

modules/busco/main.nf

@@ -0,0 +1,83 @@
+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(fasta, stageAs: 'tmp_input/*') // Required: meta map, and fasta sequence files
+ each lineage // Required: lineage to check against
+ 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_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 \\
+ --lineage_dataset $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
+ """
+}

modules/busco/meta.yml

@@ -0,0 +1,57 @@
+name: busco
+description: Benchmarking Universal Single Copy Orthologs
+keywords:
+ - quality control
+ - genome
+ - transcriptome
+ - proteome
+tools:
+ - busco:
+ description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
+ homepage: https://busco.ezlab.org/
+ documentation: https://busco.ezlab.org/busco_userguide.html
+ tool_dev_url: https://gitlab.com/ezlab/busco
+ doi: "10.1007/978-1-4939-9173-0_14"
+ licence: ["MIT"]
+
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - fasta:
+ type: file
+ description: Nucleic or amino acid sequence file in FASTA format.
+ pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+ - lineage:
+ type: value
+ description: The BUSCO lineage to use.
+ - busco_lineages_path:
+ type: directory
+ description: Path to local BUSCO lineages directory.
+ - config_file:
+ type: file
+ description: Path to BUSCO config file.
+
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - busco_dir:
+ type: directory
+ description: BUSCO lineage specific output
+ pattern: "*-busco"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+
+authors:
+ - "@priyanka-surana"
+ - "@charles-plessy"
+ - "@mahesh-panchal"
+ - "@muffato"
+ - "@jvhagey"

tests/config/pytest_modules.yml

@@ -337,6 +337,10 @@ bracken/bracken:
  - modules/bracken/bracken/**
  - tests/modules/bracken/bracken/**
 
+busco:
+ - modules/busco/**
+ - tests/modules/busco/**
+
 bwa/aln:
  - modules/bwa/aln/**
  - tests/modules/bwa/aln/**