changed process names

UPHL-BioNGS · Dec 5, 2024 · b63b57f · b63b57f
1 parent 363eb13
commit b63b57f
Showing 1 changed file with 21 additions and 19 deletions.
diff --git a/subworkflows/local/sarscov2.nf b/subworkflows/local/sarscov2.nf
@@ -1,46 +1,48 @@
-include { FREYJA                        } from '../modules/local/freyja'  
-include { FREYJA_AGGREGATE as AGGREGATE } from '../modules/local/freyja'  
-include { PANGOLIN                      } from '../modules/local/pangolin'  
-include { PANGO_ALIASOR                 } from '../modules/local/pango_aliasor' 
-include { NEXTCLADE                     } from '../modules/local/nextclade' 
-include { NEXTCLADE_DATASET as DATASET  } from '../modules/local/nextclade' 
-include { UNZIP                         } from '../modules/local/local' 
-include { VADR                          } from '../modules/local/vadr'
-
-workflow sarscov2 {
+include { FREYJA                        } from '../../modules/local/freyja'  
+include { FREYJA_AGGREGATE as AGGREGATE } from '../../modules/local/freyja'  
+include { PANGOLIN                      } from '../../modules/local/pangolin'  
+include { PANGO_ALIASOR                 } from '../../modules/local/pango_aliasor' 
+include { NEXTCLADE                     } from '../../modules/local/nextclade' 
+include { NEXTCLADE_DATASET as DATASET  } from '../../modules/local/nextclade' 
+include { UNZIP                         } from '../../modules/local/local' 
+include { VADR                          } from '../../modules/local/vadr'
+
+workflow SARSCOV2 {
     take:
         ch_fastas
         ch_bam
         ch_reference_genome
         ch_input_dataset
-        ch_freyja_script
+        ch_script
 
     main:
         ch_versions = Channel.empty()
 
         VADR(ch_fastas.collect())
-        PANGOLIN(ch_fastas.collect())
-        PANGO_ALIASOR(pangolin.out.pangolin_file)
-
         ch_versions = ch_versions.mix(VADR.out.versions)
+
+        PANGOLIN(ch_fastas.collect())
         ch_versions = ch_versions.mix(PANGOLIN.out.versions)
+
+        PANGO_ALIASOR(pangolin.out.pangolin_file)
         ch_versions = ch_versions.mix(PANGO_ALIASOR.out.versions)
 
         if ( params.download_nextclade_dataset ) {
             DATASET()
             ch_dataset = DATASET.out.dataset
-            ch_versions = ch_versions.mix(dataset.out.versions)
+            ch_versions = ch_versions.mix(DATASET.out.versions)
         } else {
             UNZIP(ch_input_dataset)
-            ch_dataset = unzip.out.dataset
+            ch_dataset = UNZIP.out.dataset
         }
 
         NEXTCLADE(ch_fastas.collect(), ch_dataset)
-        FREYJA(ch_bam.map{it -> tuple(it[0], it[1])}.combine(ch_reference_genome))
-        AGGREGATE(freyja_demix.out.demix.collect(), ch_freyja_script)
-
         ch_versions = ch_versions.mix(NEXTCLADE.out.versions)
+
+        FREYJA(ch_bam.map{it -> tuple(it[0], it[1])}.combine(ch_reference_genome))
         ch_versions = ch_versions.mix(FREYJA.out.versions.first())
+
+        AGGREGATE(FREYJA.out.demix.collect(), ch_script)
         ch_versions = ch_versions.mix(AGGREGATE.out.versions)
 
     emit: