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1 changed files with 7 additions and 7 deletions
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@ -17,7 +17,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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."
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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."
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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"
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/*
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@ -212,34 +212,34 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "clipmerge") )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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}
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if (params.longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "clip") )
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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}
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if (params.shortread_complexityfilter){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "complex") )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.run_kraken2) {
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]).dump(tag: "kraken") )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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}
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if (params.run_malt) {
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]).dump(tag: "malt") )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
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}
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// TODO Versions for Karken/MALT not report?
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// TODO create multiQC module for metaphlan
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MULTIQC (
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ch_multiqc_files.collect().dump(tag: "input_to_mqc")
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ch_multiqc_files.collect()
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)
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multiqc_report = MULTIQC.out.report.toList()
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ch_versions = ch_versions.mix(MULTIQC.out.versions)
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