mirror of
https://github.com/MillironX/taxprofiler.git
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Add kaiju2table to taxprofiler
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parent
bc84afe80d
commit
d082d67bcb
7 changed files with 135 additions and 7 deletions
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@ -289,4 +289,14 @@ process {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KAIJU_KAIJU2TABLE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${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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}
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@ -36,6 +36,9 @@
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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},
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"kaiju/kaiju2table": {
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"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
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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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@ -62,4 +65,4 @@
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}
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}
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}
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}
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}
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40
modules/nf-core/modules/kaiju/kaiju2table/main.nf
generated
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40
modules/nf-core/modules/kaiju/kaiju2table/main.nf
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@ -0,0 +1,40 @@
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process KAIJU_KAIJU2TABLE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
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'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
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input:
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tuple val(meta), path(results)
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path db
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val taxon_rank
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output:
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tuple val(meta), path('*.txt'), emit: summary
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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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dbnodes=`find -L ${db} -name "*nodes.dmp"`
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dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
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kaiju2table $args \\
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-t \$dbnodes \\
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-n \$dbname \\
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-r ${taxon_rank} \\
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-o ${prefix}.txt \\
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${results}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
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END_VERSIONS
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"""
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}
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50
modules/nf-core/modules/kaiju/kaiju2table/meta.yml
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50
modules/nf-core/modules/kaiju/kaiju2table/meta.yml
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@ -0,0 +1,50 @@
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name: "kaiju_kaiju2table"
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description: write your description here
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keywords:
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- classify
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- metagenomics
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tools:
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- kaiju:
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description: Fast and sensitive taxonomic classification for metagenomics
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homepage: https://kaiju.binf.ku.dk/
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documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
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tool_dev_url: https://github.com/bioinformatics-centre/kaiju
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doi: "10.1038/ncomms11257"
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licence: ["GNU 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 kaiju classification results
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pattern: "*.{txt}"
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- taxon_rank:
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type: string
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description: |
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Taxonomic rank to display in report
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pattern: "phylum|class|order|family|genus|species"
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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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- results:
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type: file
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description: |
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Summary table for a given taxonomic rank
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pattern: "*.{tsv}"
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authors:
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- "@sofstam"
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- "@talnor"
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- "@jfy133"
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@ -107,6 +107,7 @@ params {
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// kaiju
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run_kaiju = false
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kaiju_taxon_name = 'species'
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}
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// Load base.config by default for all pipelines
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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 +400,10 @@
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},
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"malt_generatemegansummary": {
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"type": "boolean"
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},
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"kaiju_taxon_name": {
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"type": "string",
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"default": "species"
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}
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}
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}
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}
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@ -9,6 +9,7 @@ include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/cent
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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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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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workflow PROFILING {
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take:
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@ -155,8 +156,11 @@ workflow PROFILING {
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}
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if ( params.run_kaiju ) {
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db )
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
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KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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}
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emit:
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