mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 09:09:55 +00:00
Make adapter and quality trimming optional
This commit is contained in:
parent
24a01529f5
commit
c97de32434
2 changed files with 10 additions and 3 deletions
|
@ -57,6 +57,7 @@ params {
|
|||
// FASTQ preprocessing
|
||||
fastp_clip_merge = false
|
||||
fastp_exclude_unmerged = true
|
||||
remove_adapters = false
|
||||
|
||||
// MALT
|
||||
run_malt = false
|
||||
|
|
|
@ -104,9 +104,16 @@ workflow TAXPROFILER {
|
|||
FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
|
||||
}
|
||||
|
||||
LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore )
|
||||
ch_multiqc_files = Channel.empty()
|
||||
|
||||
if ( params.remove_adapters ) {
|
||||
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
|
||||
.map { it -> [ it[0], [it[1]] ] }
|
||||
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
|
||||
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
|
||||
} else {
|
||||
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
|
||||
}
|
||||
|
||||
//
|
||||
// PERFORM RUN MERGING
|
||||
|
@ -138,6 +145,7 @@ workflow TAXPROFILER {
|
|||
|
||||
// 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
|
||||
.mix( ch_longreads_preprocessed )
|
||||
.combine(DB_CHECK.out.dbs)
|
||||
.dump(tag: "reads_plus_db")
|
||||
.branch {
|
||||
|
@ -189,13 +197,11 @@ workflow TAXPROFILER {
|
|||
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
|
||||
ch_workflow_summary = Channel.value(workflow_summary)
|
||||
|
||||
ch_multiqc_files = Channel.empty()
|
||||
ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
||||
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
|
||||
if (params.fastp_clip_merge) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue