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Merge pull request #188 from nf-core/bracken-mergetables
Add Bracken mergetables
This commit is contained in:
commit
be85cb408c
5 changed files with 110 additions and 5 deletions
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@ -321,12 +321,21 @@ process {
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]
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS {
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withName: BRACKEN_COMBINEBRACKENOUTPUTS {
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ext.prefix = { "bracken_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/bracken/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
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ext.prefix = { "kraken2_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/kraken2/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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pattern: '*.txt'
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]
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}
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@ -30,6 +30,11 @@
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"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
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"installed_by": ["modules"]
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},
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"bracken/combinebrackenoutputs": {
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"branch": "master",
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"git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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37
modules/nf-core/bracken/combinebrackenoutputs/main.nf
generated
Normal file
37
modules/nf-core/bracken/combinebrackenoutputs/main.nf
generated
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@ -0,0 +1,37 @@
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process BRACKEN_COMBINEBRACKENOUTPUTS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
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'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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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 ?: "${meta.id}"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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"""
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combine_bracken_outputs.py \\
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$args \\
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--files ${input} \\
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-o ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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combine_bracken_output: ${VERSION}
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END_VERSIONS
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"""
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}
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41
modules/nf-core/bracken/combinebrackenoutputs/meta.yml
generated
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41
modules/nf-core/bracken/combinebrackenoutputs/meta.yml
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@ -0,0 +1,41 @@
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name: "bracken_combinebrackenoutputs"
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description: Combine output of metagenomic samples analyzed by bracken.
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keywords:
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- sort
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tools:
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- "bracken":
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description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
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homepage: https://ccb.jhu.edu/software/bracken/
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documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
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tool_dev_url: https://github.com/jenniferlu717/Bracken
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doi: "10.7717/peerj-cs.104"
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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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- input:
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type: file
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description: List of output files from bracken
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pattern: "*"
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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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- txt:
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type: file
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description: Combined output in table format
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pattern: "*.txt"
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authors:
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- "@jfy133"
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@ -2,6 +2,7 @@
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// Standardise output files e.g. aggregation
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//
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include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
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include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
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include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
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@ -25,10 +26,11 @@ workflow STANDARDISATION_PROFILES {
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*/
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ch_input_profiles = profiles
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.branch {
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motus: it[0]['tool'] == 'motus'
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kraken2: it[0]['tool'] == 'kraken2'
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bracken: it[0]['tool'] == 'bracken'
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centrifuge: it[0]['tool'] == 'centrifuge'
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kraken2: it[0]['tool'] == 'kraken2'
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metaphlan3: it[0]['tool'] == 'metaphlan3'
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motus: it[0]['tool'] == 'motus'
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unknown: true
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}
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@ -49,7 +51,18 @@ workflow STANDARDISATION_PROFILES {
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Standardise and aggregate
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*/
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// CENTRIFUGE
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// Bracken
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ch_profiles_for_bracken = ch_input_profiles.bracken
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple()
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.map {
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[[id:it[0]], it[1]]
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}
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BRACKEN_COMBINEBRACKENOUTPUTS ( ch_profiles_for_bracken )
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// CENTRIFUGE
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// Collect and replace id for db_name for prefix
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// Have to sort by size to ensure first file actually has hits otherwise
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