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Busco module commit with nf-core v2.2 c1
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42
modules/busco/main.nf
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42
modules/busco/main.nf
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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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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 $fasta > __UNCOMPRESSED_FASTA_FILE__
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# Copy the image's AUGUSTUS config directory if it was not provided to the module
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[ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
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AUGUSTUS_CONFIG_PATH=augustus_config \\
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busco \\
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$args \\
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--augustus \\
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--cpu $task.cpus \\
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--in __UNCOMPRESSED_FASTA_FILE__ \\
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--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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52
modules/busco/meta.yml
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52
modules/busco/meta.yml
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name: busco
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description: Benchmarking Universal Single Copy Orthologs
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keywords:
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- quality control
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- genome
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- transcriptome
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- proteome
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tools:
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- busco:
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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.
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homepage: https://busco.ezlab.org/
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documentation: https://busco.ezlab.org/busco_userguide.html
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tool_dev_url: https://gitlab.com/ezlab/busco
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doi: "10.1007/978-1-4939-9173-0_14"
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licence: ['MIT']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: Nucleic or amino acid sequence file in FASTA format
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pattern: "*.{fasta}"
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- augustus_config:
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type: directory
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description: AUGUSTUS config directory
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- tsv:
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type: file
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description: Full summary table
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pattern: "*.{tsv}"
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- txt:
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type: file
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description: Short summary text
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pattern: "*.{txt}"
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authors:
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- "@priyanka-surana"
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- "@charles-plessy"
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@ -230,6 +230,10 @@ bowtie2/build:
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- modules/bowtie2/build/**
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- tests/modules/bowtie2/build_test/**
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busco:
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- modules/busco/**
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- tests/modules/busco/**
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bwa/aln:
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- modules/bwa/aln/**
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- tests/modules/bwa/aln/**
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26
tests/modules/busco/main.nf
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26
tests/modules/busco/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
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include { BUSCO as BUSCO_CHR22 } from '../../../modules/busco/main.nf'
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include { UNTAR } from '../../../modules/untar/main.nf'
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// This tests genome decompression, empty input channels and data download
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workflow test_busco_bacteroidales {
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input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
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BUSCO_BACTE ( input,
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[],
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[] )
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}
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// This tests uncompressed genome, BUSCO lineage file provided via input channel, and offline mode
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workflow test_busco_chr22 {
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input = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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lineage_dataset = [ file(params.test_data['homo_sapiens']['genome']['chr22_odb10_tar_gz'], checkIfExists: true) ]
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UNTAR(lineage_dataset)
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BUSCO_CHR22 ( input,
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[],
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UNTAR.out.untar )
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}
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5
tests/modules/busco/nextflow.config
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5
tests/modules/busco/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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20
tests/modules/busco/test.yml
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20
tests/modules/busco/test.yml
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- name: busco test_busco_bacteroidales
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command: nextflow run ./tests/modules/busco -entry test_busco_bacteroidales -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
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tags:
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- busco
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files:
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- path: output/busco/test/run_bacteroidales_odb10/full_table.tsv
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md5sum: 8d7b401d875ecd9291b01bf4485bf080
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- path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
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contains: ['Complete BUSCOs (C)']
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- name: busco test_busco_chr22
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command: nextflow run ./tests/modules/busco -entry test_busco_chr22 -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
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tags:
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- busco
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files:
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- path: output/busco/test/run_chr22_odb10/full_table.tsv
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md5sum: 83f20e8996c591338ada73b6ab0eb269
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- path: output/busco/test/run_chr22_odb10/short_summary.txt
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contains: ['Complete BUSCOs (C)']
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