mirror of
https://github.com/MillironX/taxprofiler.git
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Merge pull request #47 from nf-core/profiling-subworkflow
Move profiling to subworkflow
This commit is contained in:
James A. Fellows Yates
GitHub
commit
dd22e042be
4 changed files with 142 additions and 102 deletions
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@ -167,7 +167,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{rma6,tab,text,sam,log}'
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pattern: '*.{log}'
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]
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}
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@ -177,7 +177,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,txt}'
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pattern: '*.{txt}'
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]
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}
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@ -190,6 +190,16 @@ process {
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.txt'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -198,14 +208,12 @@ process {
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]
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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withName: MULTIQC {
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,txt}'
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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}
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119
subworkflows/local/profiling.nf
Normal file
119
subworkflows/local/profiling.nf
Normal file
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@ -0,0 +1,119 @@
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//
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// Run profiling
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//
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include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/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 { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
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workflow PROFILING {
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take:
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shortreads // [ [ meta ], [ reads ] ]
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longreads // [ [ meta ], [ reads ] ]
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databases // [ [ meta ], path ]
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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*/
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// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
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ch_input_for_profiling = shortreads
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.mix( longreads )
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.combine(databases)
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.branch {
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malt: it[2]['tool'] == 'malt'
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kraken2: it[2]['tool'] == 'kraken2'
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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centrifuge: it[2]['tool'] == 'centrifuge'
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unknown: true
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}
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/*
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PREPARE PROFILER INPUT CHANNELS
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*/
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// Each tool as a slightly different input structure and generally separate
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// input channels for reads vs databases. We restructure the channel tuple
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// for each tool and make liberal use of multiMap to keep reads/databases
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// channel element order in sync with each other
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// MALT: We groupTuple to have all samples in one channel for MALT as database
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// loading takes a long time, so we only want to run it once per database
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// TODO document somewhere we only accept illumina short reads for MALT?
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ch_input_for_malt = ch_input_for_profiling.malt
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def db = it[3]
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[ temp_meta, it[1], db ]
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}
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.groupTuple(by: [0,2])
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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db: it[2]
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}
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// All subsequent tools can easily run on a per-sample basis
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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/*
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RUN PROFILING
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*/
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if ( params.run_malt ) {
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
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}
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if ( params.run_kraken2 ) {
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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}
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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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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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}
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if ( params.run_metaphlan3 ) {
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METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
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}
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emit:
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// TODO work out if there is enough standardisation of output to export as one?
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//output = ch_filtered_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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@ -10,7 +10,7 @@ workflow SHORTREAD_FASTP {
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reads // [[meta], [reads]]
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main:
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ch_versions = Channel.empty()
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_input_for_fastp = reads
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@ -44,6 +44,7 @@ include { DB_CHECK } from '../subworkflows/local/db_check'
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include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
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include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
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include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
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include { PROFILING } from '../subworkflows/local/profiling'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -59,10 +60,6 @@ include { MULTIQC } from '../modules/nf-core/modules/multiqc
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
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include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
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include { MALT_RUN } from '../modules/nf-core/modules/malt/run/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 { METAPHLAN3 } from '../modules/nf-core/modules/metaphlan3/main'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -88,6 +85,7 @@ workflow TAXPROFILER {
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DB_CHECK (
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ch_databases
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)
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ch_versions = ch_versions.mix(DB_CHECK.out.versions)
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/*
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MODULE: Run FastQC
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@ -104,6 +102,7 @@ workflow TAXPROFILER {
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.shortread_clipmerge ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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@ -127,88 +126,11 @@ workflow TAXPROFILER {
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}
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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SUBWORKFLOW: PROFILING
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*/
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// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
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ch_input_for_profiling = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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.combine(DB_CHECK.out.dbs)
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.branch {
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malt: it[2]['tool'] == 'malt'
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kraken2: it[2]['tool'] == 'kraken2'
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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centrifuge: it[2]['tool'] == 'centrifuge'
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unknown: true
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}
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/*
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PREPARE PROFILER INPUT CHANNELS
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*/
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// We groupTuple to have all samples in one channel for MALT as database
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// loading takes a long time, so we only want to run it once per database
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// TODO document somewhere we only accept illumina short reads for MALT?
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ch_input_for_malt = ch_input_for_profiling.malt
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def db = it[3]
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[ temp_meta, it[1], db ]
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}
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.groupTuple(by: [0,2])
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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db: it[2]
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}
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// We can run Kraken2 one-by-one sample-wise
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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// We can run centrifuge one-by-one sample-wise
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.dump(tag: "input for centrifuge")
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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//
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// RUN PROFILING
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//
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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/*
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MODULE: RUN PROFILING
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*/
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if ( params.run_malt ) {
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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}
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if ( params.run_kraken2 ) {
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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}
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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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}
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if ( params.run_metaphlan3 ) {
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METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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}
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PROFILING ( ch_shortreads_filtered, ch_longreads_preprocessed, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( PROFILING.out.versions )
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/*
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MODULE: MultiQC
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@ -244,17 +166,8 @@ workflow TAXPROFILER {
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.run_kraken2) {
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
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if (params.run_malt) {
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
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}
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// TODO Versions for Karken/MALT not report?
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// TODO create multiQC module for metaphlan
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MULTIQC (
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ch_multiqc_files.collect()
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