millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-09-21 07:52:03 +00:00
Code Issues Releases Packages Activity

Include long reads preprocessing subworkflow

Browse source
This commit is contained in:
ljmesi 2022-03-18 15:12:07 +01:00
parent 1e42f1d9f2
commit 582aaa105f
1 changed files with 6 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

7
workflows/taxprofiler.nf
View file

@ -40,7 +40,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check'
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 )
}
LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore )
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
//
// 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(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)
}