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Add some debugging notes

This commit is contained in:
James A. Fellows Yates 2022-03-26 20:54:50 +00:00
parent 622fafedc8
commit e6e8ed7cc9
2 changed files with 34 additions and 30 deletions

View file

@ -105,7 +105,7 @@ process {
pattern: '*.{rma6,tab,text,sam,log}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: KRAKEN2_KRAKEN2 {
@ -115,7 +115,7 @@ process {
pattern: '*.{fastq.gz,txt}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: CUSTOM_DUMPSOFTWAREVERSIONS {

View file

@ -74,9 +74,9 @@ workflow TAXPROFILER {
ch_versions = Channel.empty()
//
// SUBWORKFLOW: Read in samplesheet, validate and stage input files
//
/*
SUBWORKFLOW: Read in samplesheet, validate and stage input files
*/
INPUT_CHECK (
ch_input
)
@ -86,9 +86,9 @@ workflow TAXPROFILER {
ch_databases
)
//
// MODULE: Run FastQC
//
/*
MODULE: Run FastQC
*/
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
FASTQC (
ch_input_for_fastqc
@ -99,9 +99,9 @@ workflow TAXPROFILER {
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
//
// PERFORM PREPROCESSING
//
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
if ( params.shortread_clipmerge ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
} else {
@ -116,16 +116,19 @@ workflow TAXPROFILER {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
}
//
// PERFORM SHORT READ RUN MERGING
/*
MODULE: PERFORM SHORT READ RUN MERGING
*/
// TODO: Check not necessary for long reads too?
//
// TODO: source of clash - combined should only occur when
// files ARE to be combined. SE/unmerged (see not below)
ch_processed_for_combine = ch_shortreads_preprocessed
.dump(tag: "prep_for_combine_grouping")
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['run_accession'] = 'combined'
//meta_new['run_accession'] = 'combined'
[ meta_new, reads ]
}
.groupTuple ( by: 0 )
@ -134,17 +137,18 @@ workflow TAXPROFILER {
skip: it[1].size() < 2
}
// NOTE: this does not allow CATing of SE & PE runs of same sample
// when --shortread_clipmerge_mergepairs is false
CAT_FASTQ ( ch_processed_for_combine.combine )
// TODO May need to flatten reads?
ch_reads_for_profiling = ch_processed_for_combine.skip
.dump(tag: "skip_combine")
.mix( CAT_FASTQ.out.reads )
.dump(tag: "files_for_profiling")
//
// COMBINE READS WITH POSSIBLE DATABASES
//
/*
COMBINE READS WITH POSSIBLE DATABASES
*/
// 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]
ch_input_for_profiling = ch_reads_for_profiling
@ -157,9 +161,9 @@ workflow TAXPROFILER {
unknown: true
}
//
// PREPARE PROFILER INPUT CHANNELS
//
/*
PREPARE PROFILER INPUT CHANNELS
*/
// We groupTuple to have all samples in one channel for MALT as database
// loading takes a long time, so we only want to run it once per database
@ -171,7 +175,7 @@ workflow TAXPROFILER {
[ temp_meta, it[1], db ]
}
.groupTuple(by: [0,2])
.dump(tag: "input_for_malt")
.dump(tag: "input_to_malt")
.multiMap {
it ->
reads: [ it[0], it[1].flatten() ]
@ -180,16 +184,16 @@ workflow TAXPROFILER {
// We can run Kraken2 one-by-one sample-wise
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "input_for_kraken")
.dump(tag: "input_to_kraken")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1].flatten() ]
db: it[3]
}
//
// RUN PROFILING
//
/*
MODULE: RUN PROFILING
*/
if ( params.run_malt ) {
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
}
@ -198,9 +202,9 @@ workflow TAXPROFILER {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
}
//
// MODULE: MultiQC
//
/*
MODULE: MultiQC
*/
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)