trying to pass kraken2 report to multiqc

Author: ctuni

modules.json

@@ -8,32 +8,44 @@
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "krona/ktupdatetaxonomy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -42,20 +54,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}

subworkflows/local/phylogenetic_qc.nf

@@ -13,6 +13,8 @@ workflow PHYLOGENETIC_QC{
 
     main:
     ch_reads = reads
+    ch_multiqc_files = Channel.empty()
+    ch_versions             = Channel.empty()
     //
     // MODULE: Untar kraken2_db
     //
@@ -28,6 +30,8 @@ workflow PHYLOGENETIC_QC{
         params.kraken2_save_reads,
         params.kraken2_save_readclassifications
     )
+    ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
+    ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
     //KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect()
 
     //
@@ -40,5 +44,6 @@ workflow PHYLOGENETIC_QC{
     )
 
     emit:
-    kraken2_report = KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect()
+    versions        = ch_versions
+    mqc             = ch_multiqc_files
 }

workflows/seqinspector.nf

@@ -40,6 +40,7 @@ workflow SEQINSPECTOR {
         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
@@ -48,8 +49,9 @@ workflow SEQINSPECTOR {
         ch_samplesheet
     )
 
-    ch_multiqc_files = ch_multiqc_files.mix(PHYLOGENETIC_QC.out.kraken2_report)
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix(PHYLOGENETIC_QC.out.mqc.collect{it[1]}.ifEmpty([]))
+    ch_versions = ch_versions.mix(PHYLOGENETIC_QC.out.versions)
+
 
     //
     // Collate and save software versions