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https://github.com/MillironX/taxprofiler.git
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Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
This commit is contained in:
parent
db688575f6
commit
c8dbf5be47
5 changed files with 108 additions and 1 deletions
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@ -294,6 +294,15 @@ process {
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]
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]
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}
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS {
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ext.prefix = { "${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/kraken2/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: KRONA_CLEANUP {
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withName: KRONA_CLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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publishDir = [
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@ -73,6 +73,10 @@
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"branch": "master",
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"branch": "master",
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"git_sha": "409a308ba46284d8ebb48c2c1befd6f6433db3f7"
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"git_sha": "409a308ba46284d8ebb48c2c1befd6f6433db3f7"
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},
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},
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"krakentools/combinekreports": {
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"branch": "master",
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"git_sha": "ee0346b4d14ffdc15ce7e093ca1363cd07c9bd78"
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},
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"krakentools/kreport2krona": {
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"krakentools/kreport2krona": {
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"branch": "master",
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"branch": "master",
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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34
modules/nf-core/modules/krakentools/combinekreports/main.nf
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34
modules/nf-core/modules/krakentools/combinekreports/main.nf
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@ -0,0 +1,34 @@
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process KRAKENTOOLS_COMBINEKREPORTS {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(kreports)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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combine_kreports.py \\
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-r ${kreports} \\
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-o ${prefix}.txt \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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combine_kreports.py: ${VERSION}
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END_VERSIONS
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"""
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}
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43
modules/nf-core/modules/krakentools/combinekreports/meta.yml
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43
modules/nf-core/modules/krakentools/combinekreports/meta.yml
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name: krakentools_combinekreports
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description: Takes a Kraken report file and prints out a krona-compatible TEXT file
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keywords:
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- kraken
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- krakentools
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- metagenomics
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- table
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- combining
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- merging
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tools:
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- krakentools:
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description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
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homepage: https://github.com/jenniferlu717/KrakenTools
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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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- kreports:
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type: file
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description: List of kraken-style report files
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pattern: "*.{txt,kreport}"
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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 kreport file of all input files
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pattern: "*.txt"
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authors:
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- "@jfy133"
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@ -3,7 +3,8 @@
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//
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//
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
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include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
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include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
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workflow STANDARDISATION_PROFILES {
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workflow STANDARDISATION_PROFILES {
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take:
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take:
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@ -23,6 +24,7 @@ workflow STANDARDISATION_PROFILES {
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ch_input_profiles = profiles
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ch_input_profiles = profiles
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.branch {
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.branch {
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motus: it[0]['tool'] == 'motus'
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motus: it[0]['tool'] == 'motus'
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kraken2: it[0]['tool'] == 'kraken2'
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unknown: true
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unknown: true
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}
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}
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@ -58,6 +60,21 @@ workflow STANDARDISATION_PROFILES {
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
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// Kraken2
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// Collect and replace id for db_name for prefix
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ch_profiles_for_kraken2 = ch_input_profiles.kraken2
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple(sort: {-it.size()} )
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.map {
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[[id:it[0]], it[1]]
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}
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KRAKENTOOLS_COMBINEKREPORTS ( ch_profiles_for_kraken2 )
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ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions )
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// mOTUs has a 'single' database, and cannot create custom ones.
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// mOTUs has a 'single' database, and cannot create custom ones.
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// Therefore removing db info here, and publish merged at root mOTUs results
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// Therefore removing db info here, and publish merged at root mOTUs results
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// directory
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// directory
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