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https://github.com/MillironX/taxprofiler.git
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Add centrifuge kreport in taxprofiler
This commit is contained in:
parent
63230c3254
commit
c00ca1c2b8
7 changed files with 118 additions and 9 deletions
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@ -254,6 +254,16 @@ process {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CENTRIFUGE_KREPORT {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -21,6 +21,9 @@
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"centrifuge/centrifuge": {
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"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
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},
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"centrifuge/kreport": {
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"git_sha": "be4ae28c3c95b3c4047a7d9fb4cb0ed749631cea"
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},
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"custom/dumpsoftwareversions": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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@ -30,6 +33,9 @@
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"fastqc": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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},
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"kraken2/kraken2": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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@ -53,9 +59,6 @@
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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},
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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}
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}
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}
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33
modules/nf-core/modules/centrifuge/kreport/main.nf
generated
Normal file
33
modules/nf-core/modules/centrifuge/kreport/main.nf
generated
Normal file
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@ -0,0 +1,33 @@
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process CENTRIFUGE_KREPORT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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container "${ 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(results)
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path db
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output:
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tuple val(meta), path('*.txt') , emit: kreport
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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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"""
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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41
modules/nf-core/modules/centrifuge/kreport/meta.yml
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41
modules/nf-core/modules/centrifuge/kreport/meta.yml
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@ -0,0 +1,41 @@
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name: "centrifuge_kreport"
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description: Creates Kraken-style reports from centrifuge out files
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keywords:
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- metagenomics
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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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- results:
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type: file
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description: File containing the centrifuge classification results
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pattern: "*.{txt}"
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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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- kreport:
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type: file
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description: |
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File containing kraken-style report from centrifuge
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out files.
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pattern: "*.{txt}"
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authors:
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- "@sofstam"
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- "@jfy133"
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@ -98,6 +98,7 @@ params {
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// centrifuge
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run_centrifuge = false
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centrifuge_kreport = false
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centrifuge_save_unaligned = false
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centrifuge_save_aligned = false
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centrifuge_sam_format = false
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@ -10,7 +10,10 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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@ -294,7 +304,10 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -335,7 +348,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -384,6 +400,9 @@
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},
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"malt_generatemegansummary": {
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"type": "boolean"
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},
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"centrifuge_kreport": {
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"type": "boolean"
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}
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}
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}
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@ -6,6 +6,7 @@ include { MALT_RUN } from '../../modules/nf-core/modules/malt
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include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main'
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
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include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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@ -142,8 +143,9 @@ workflow PROFILING {
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if ( params.run_centrifuge ) {
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_CENTRIFUGE.out.report )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
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}
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if ( params.run_metaphlan3 ) {
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