added output to multiqc

nf-core · Oct 28, 2024 · c5edd67 · c5edd67
1 parent 033df6e
commit c5edd67
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/subworkflows/local/phylogenetic_qc.nf b/subworkflows/local/phylogenetic_qc.nf
@@ -28,14 +28,14 @@ workflow PHYLOGENETIC_QC{
         params.kraken2_save_reads,
         params.kraken2_save_readclassifications
     )
-    KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect()
+    //KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect()
 
     //
     // MODULE: krona plot the kraken2 reports
     //
     KRONA_KTUPDATETAXONOMY()
     KRONA_KTIMPORTTAXONOMY (
-        KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect(),
+        KRAKEN2_KRAKEN2.out.report,
         KRONA_KTUPDATETAXONOMY.out.db
     )
 

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
@@ -39,8 +39,6 @@ workflow SEQINSPECTOR {
     FASTQC (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
     // SUBWORKFLOW: Run kraken2 and produce krona plots
@@ -49,6 +47,10 @@ workflow SEQINSPECTOR {
         ch_samplesheet
     )
 
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip).mix(PHYLOGENETIC_QC.out.kraken2_report)
+    ch_multiqc_files.view()
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+
     //
     // Collate and save software versions
     //