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Include long reads preprocessing subworkflow

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ljmesi 2022-03-18 15:12:07 +01:00
parent 1e42f1d9f2
commit 582aaa105f
1 changed files with 6 additions and 1 deletions
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7
workflows/taxprofiler.nf
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@ -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)
} }