diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index eb2b461..8dfe996 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -17,7 +17,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true // Check mandatory parameters if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } -if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not except uncollapsed paired-reads. Pairs will be profiled as separate files." +if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files." if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs" /* @@ -212,34 +212,34 @@ 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: "clipmerge") ) + 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: "clip") ) + 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: "complex") ) + 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: "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: "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() ) } // TODO Versions for Karken/MALT not report? // TODO create multiQC module for metaphlan MULTIQC ( - ch_multiqc_files.collect().dump(tag: "input_to_mqc") + ch_multiqc_files.collect() ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions)