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Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory
Delete extra unnecessary directory
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commit
1ac5a129a8
2 changed files with 0 additions and 127 deletions
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process CENTRIFUGE_CENTRIFUGE {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
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'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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input:
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tuple val(meta), path(reads)
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path db
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val save_unaligned
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val save_aligned
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val sam_format
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output:
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tuple val(meta), path('*report.txt') , emit: report
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tuple val(meta), path('*results.txt') , emit: results
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tuple val(meta), path('*.sam') , optional: true, emit: sam
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tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
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tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
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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}"
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def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
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def unaligned = ''
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def aligned = ''
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if (meta.single_end) {
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unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
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} else {
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unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
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}
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def sam_output = sam_format ? "--out-fmt 'sam'" : ''
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"""
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## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge \\
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-x \$db_name \\
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-p $task.cpus \\
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$paired \\
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--report-file ${prefix}.report.txt \\
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-S ${prefix}.results.txt \\
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$unaligned \\
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$aligned \\
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$sam_output \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
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END_VERSIONS
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"""
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}
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name: centrifuge_centrifuge
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description: Classifies metagenomic sequence data
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keywords:
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- classify
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- metagenomics
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- fastq
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- db
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tools:
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- centrifuge:
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description: Centrifuge is a classifier for metagenomic sequences.
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homepage: https://ccb.jhu.edu/software/centrifuge/
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documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
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doi: 10.1101/gr.210641.116
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licence: ["GPL v3"]
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- db:
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type: directory
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description: Path to directory containing centrifuge database files
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- save_unaligned:
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type: value
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description: If true unmapped fastq files are saved
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- save_aligned:
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type: value
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description: If true mapped fastq files are saved
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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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- report:
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type: file
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description: |
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File containing a classification summary
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pattern: "*.{report.txt}"
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- results:
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type: file
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description: |
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File containing classification results
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pattern: "*.{results.txt}"
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- fastq_unmapped:
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type: file
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description: Unmapped fastq files
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pattern: "*.unmapped.fastq.gz"
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- fastq_mapped:
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type: file
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description: Mapped fastq files
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pattern: "*.mapped.fastq.gz"
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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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authors:
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- "@sofstam"
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- "@jfy133"
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- "@sateeshperi"
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