mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:23:09 +00:00
Include long reads preprocessing subworkflow
This commit is contained in:
parent
1e42f1d9f2
commit
582aaa105f
1 changed files with 6 additions and 1 deletions
|
@ -40,7 +40,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
|
||||||
|
|
||||||
include { DB_CHECK } from '../subworkflows/local/db_check'
|
include { DB_CHECK } from '../subworkflows/local/db_check'
|
||||||
include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
|
include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
|
||||||
|
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
|
||||||
|
|
||||||
/*
|
/*
|
||||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
@ -104,6 +104,10 @@ workflow TAXPROFILER {
|
||||||
FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
|
FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
|
||||||
}
|
}
|
||||||
|
|
||||||
|
LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore )
|
||||||
|
|
||||||
|
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
|
||||||
|
|
||||||
//
|
//
|
||||||
// PERFORM RUN MERGING
|
// PERFORM RUN MERGING
|
||||||
//
|
//
|
||||||
|
@ -191,6 +195,7 @@ workflow TAXPROFILER {
|
||||||
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
|
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(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(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
||||||
|
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
|
||||||
if (params.fastp_clip_merge) {
|
if (params.fastp_clip_merge) {
|
||||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
|
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
|
||||||
}
|
}
|
||||||
|
|
Loading…
Reference in a new issue