mirror of
https://github.com/MillironX/taxprofiler.git
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Add some debugging notes
This commit is contained in:
James A. Fellows Yates
parent
622fafedc8
commit
e6e8ed7cc9
2 changed files with 34 additions and 30 deletions
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@ -105,7 +105,7 @@ process {
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRAKEN2_KRAKEN2 {
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@ -115,7 +115,7 @@ process {
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pattern: '*.{fastq.gz,txt}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -74,9 +74,9 @@ workflow TAXPROFILER {
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ch_versions = Channel.empty()
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//
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// SUBWORKFLOW: Read in samplesheet, validate and stage input files
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//
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/*
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SUBWORKFLOW: Read in samplesheet, validate and stage input files
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*/
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INPUT_CHECK (
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ch_input
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)
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@ -86,9 +86,9 @@ workflow TAXPROFILER {
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ch_databases
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)
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//
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// MODULE: Run FastQC
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//
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/*
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MODULE: Run FastQC
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*/
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
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FASTQC (
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ch_input_for_fastqc
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@ -99,9 +99,9 @@ workflow TAXPROFILER {
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ch_versions.unique().collectFile(name: 'collated_versions.yml')
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)
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//
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// PERFORM PREPROCESSING
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//
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/*
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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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@ -116,16 +116,19 @@ workflow TAXPROFILER {
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
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}
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//
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// PERFORM SHORT READ RUN MERGING
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/*
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MODULE: PERFORM SHORT READ RUN MERGING
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*/
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// TODO: Check not necessary for long reads too?
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//
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// TODO: source of clash - combined should only occur when
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// files ARE to be combined. SE/unmerged (see not below)
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ch_processed_for_combine = ch_shortreads_preprocessed
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.dump(tag: "prep_for_combine_grouping")
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['run_accession'] = 'combined'
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//meta_new['run_accession'] = 'combined'
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[ meta_new, reads ]
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}
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.groupTuple ( by: 0 )
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@ -134,17 +137,18 @@ workflow TAXPROFILER {
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skip: it[1].size() < 2
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}
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// NOTE: this does not allow CATing of SE & PE runs of same sample
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// when --shortread_clipmerge_mergepairs is false
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CAT_FASTQ ( ch_processed_for_combine.combine )
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// TODO May need to flatten reads?
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ch_reads_for_profiling = ch_processed_for_combine.skip
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.dump(tag: "skip_combine")
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.mix( CAT_FASTQ.out.reads )
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.dump(tag: "files_for_profiling")
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//
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// COMBINE READS WITH POSSIBLE DATABASES
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//
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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 = ch_reads_for_profiling
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@ -157,9 +161,9 @@ workflow TAXPROFILER {
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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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/*
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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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@ -171,7 +175,7 @@ workflow TAXPROFILER {
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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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.dump(tag: "input_for_malt")
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.dump(tag: "input_to_malt")
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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@ -180,16 +184,16 @@ workflow TAXPROFILER {
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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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.dump(tag: "input_for_kraken")
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.dump(tag: "input_to_kraken")
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1].flatten() ]
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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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/*
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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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@ -198,9 +202,9 @@ workflow TAXPROFILER {
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
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}
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//
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// MODULE: MultiQC
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//
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/*
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MODULE: MultiQC
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*/
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workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
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ch_workflow_summary = Channel.value(workflow_summary)
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