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https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:23:09 +00:00
Fix MQC staging and remove debugging dump
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parent
d46ddd972c
commit
245a4d1f5d
2 changed files with 8 additions and 9 deletions
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@ -117,8 +117,8 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix(
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ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
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ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
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ADAPTERREMOVAL_PAIRED.out.log,
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ADAPTERREMOVAL_SINGLE.out.log
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)
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emit:
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@ -171,7 +171,6 @@ workflow TAXPROFILER {
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}
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.dump(tag: "input_metaphlan3")
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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@ -213,34 +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([]) )
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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_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([]) )
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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_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([]) )
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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_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([]) )
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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_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([]) )
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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_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()
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ch_multiqc_files.collect().dump(tag: "input_to_mqc")
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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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