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Code Issues Releases Packages Activity

Remove remaining debugging .dumps(

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James Fellows Yates 2022-04-02 17:07:30 +02:00
parent 7f1a7fb4e7
commit 469e4f3682
1 changed files with 6 additions and 6 deletions
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12
workflows/taxprofiler.nf
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@ -90,7 +90,7 @@ workflow TAXPROFILER {
/* /*
MODULE: Run FastQC MODULE: Run FastQC
*/ */
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq") ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
FASTQC ( FASTQC (
ch_input_for_fastqc ch_input_for_fastqc
@ -199,27 +199,27 @@ workflow TAXPROFILER {
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([]))
if (params.shortread_clipmerge) { if (params.shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_shortclipmerge") ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions ) ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
} }
if (params.longread_clip) { if (params.longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_longclipmerge") ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions ) ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
} }
if (params.shortread_complexityfilter){ if (params.shortread_complexityfilter){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_compelxity") ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions ) ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
} }
if (params.run_kraken2) { if (params.run_kraken2) {
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_kraken") ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
} }
if (params.run_malt) { if (params.run_malt) {
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_malt") ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
} }