diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index a403589..1c86edb 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -90,7 +90,7 @@ workflow TAXPROFILER { /* 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 ( ch_input_for_fastqc @@ -199,27 +199,27 @@ workflow TAXPROFILER { ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) 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 ) } 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 ) } 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 ) } 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() ) } 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() ) }