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Fix MQC staging and remove debugging dump

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This commit is contained in:
James Fellows Yates 2022-04-05 13:08:44 +02:00
parent d46ddd972c
commit 245a4d1f5d
2 changed files with 8 additions and 9 deletions
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4
subworkflows/local/shortread_adapterremoval.nf
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@ -117,8 +117,8 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() ) ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() ) ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( ch_multiqc_files = ch_multiqc_files.mix(
ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_PAIRED.out.log,
ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} ADAPTERREMOVAL_SINGLE.out.log
) )
emit: emit:

13
workflows/taxprofiler.nf
View file

@ -171,7 +171,6 @@ workflow TAXPROFILER {
} }
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3 ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.dump(tag: "input_metaphlan3")
.multiMap { .multiMap {
it -> it ->
reads: [it[0] + it[2], it[1]] reads: [it[0] + it[2], it[1]]
@ -213,34 +212,34 @@ 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([]) ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "clipmerge") )
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([]) ) ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "clip") )
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([]) ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]).dump(tag: "complex") )
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([]) ) ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]).dump(tag: "kraken") )
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([]) ) ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]).dump(tag: "malt") )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
} }
// TODO Versions for Karken/MALT not report? // TODO Versions for Karken/MALT not report?
// TODO create multiQC module for metaphlan // TODO create multiQC module for metaphlan
MULTIQC ( MULTIQC (
ch_multiqc_files.collect() ch_multiqc_files.collect().dump(tag: "input_to_mqc")
) )
multiqc_report = MULTIQC.out.report.toList() multiqc_report = MULTIQC.out.report.toList()
ch_versions = ch_versions.mix(MULTIQC.out.versions) ch_versions = ch_versions.mix(MULTIQC.out.versions)