include krakenuniq in profiling subworkflow

modules.json

@@ -89,6 +89,10 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "krakenuniq/preloadedkrakenuniq": {
+                        "branch": "master",
+                        "git_sha": "13b9d4854593c03e5e25e8a8f47462542c2c0dd4"
+                    },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"

subworkflows/local/profiling.nf

@@ -11,6 +11,7 @@ include { METAPHLAN3_METAPHLAN3                 } from '../../modules/nf-core/me
 include { KAIJU_KAIJU                           } from '../../modules/nf-core/kaiju/kaiju/main'
 include { DIAMOND_BLASTX                        } from '../../modules/nf-core/diamond/blastx/main'
 include { MOTUS_PROFILE                         } from '../../modules/nf-core/motus/profile/main'
+include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ        } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
 
 workflow PROFILING {
     take:
@@ -45,6 +46,7 @@ workflow PROFILING {
                 kaiju: it[2]['tool'] == 'kaiju'
                 diamond: it[2]['tool'] == 'diamond'
                 motus: it[2]['tool'] == 'motus'
+                krakenuniq: it[2]['tool'] == 'krakenuniq'
                 unknown: true
             }
 
@@ -228,6 +230,22 @@ workflow PROFILING {
         ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
     }
 
+    if ( params.run_krakenuniq ) {
+        ch_input_for_krakenuniq =  ch_input_for_profiling.krakenuniq
+                                    .multiMap {
+                                        it ->
+                                            reads: [ it[0] + it[2], it[1] ]
+                                            db: it[3]
+                                }
+
+        KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads, ch_input_for_krakenuniq.db, params.krakenuniq_save_reads, params.krakenuniq_save_readclassification )
+        ch_multiqc_files       = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
+        ch_versions            = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() )
+        ch_raw_classifications = ch_raw_classifications.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.classified_assignment )
+        ch_raw_profiles        = ch_raw_profiles.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
+
+    }
+
     emit:
     classifications = ch_raw_classifications
     profiles        = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom