Working subworkflow

Author: VerbalCant

conf/modules.config

@@ -1860,5 +1860,9 @@ process {
             ]
         ]
     }
-    //
+
+    // Add configuration for HAPLOGREP3_CLASSIFY in HAPLOTYPE_HUMAN_MTDNA
+    withName: 'NFCORE_EAGER:EAGER:HAPLOTYPE_HUMAN_MTDNA:HAPLOGREP3_CLASSIFY' {
+        ext.args = '--tree phylotree-fu-rcrs@1.2'
+    }
 }

…lows/local/haplotype_human_mtdna/main.nf …workflows/local/haplotype_human_mtdna.nfsubworkflows/local/haplotype_human_mtdna/main.nf renamed to subworkflows/local/haplotype_human_mtdna.nf subworkflows/local/haplotype_human_mtdna/main.nf renamed to subworkflows/local/haplotype_human_mtdna.nf

@@ -19,10 +19,6 @@ workflow HAPLOTYPE_HUMAN_MTDNA {
     // Prepare input for haplogrep3
     // The module requires a tuple with [meta, inputfile]
     ch_input_haplogrep3 = ch_mtdna_vcf
-        .map {
-            // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
-            addNewMetaFromAttributes( it, "reference", "reference", false )
-        }
 
     // Run mtDNA haplogroup classification with haplogrep3
     HAPLOGREP3_CLASSIFY(ch_input_haplogrep3)
@@ -33,6 +29,3 @@ workflow HAPLOTYPE_HUMAN_MTDNA {
     haplogroups    = ch_haplogroups    // channel: [ val(meta), path("*.txt") ]
     versions       = ch_versions       // channel: path(versions.yml)
 }
-
-
-workflow HAPLOGREP3_CLASSIFY {

subworkflows/local/haplotype_human_mtdna/meta.yml

@@ -32,7 +32,7 @@ include { METAGENOMICS                                        } from '../subwork
 include { ESTIMATE_CONTAMINATION                              } from '../subworkflows/local/estimate_contamination'
 include { CALCULATE_DAMAGE                                    } from '../subworkflows/local/calculate_damage'
 include { RUN_SEXDETERRMINE                                   } from '../subworkflows/local/run_sex_determination'
-include { CLASSIFY_MTDNA_HAPLOGROUP                           } from '../subworkflows/local/classify_mtdna_haplogroup'
+include { HAPLOTYPE_HUMAN_MTDNA                               } from '../subworkflows/local/haplotype_human_mtdna'
 include { MERGE_LIBRARIES                                     } from '../subworkflows/local/merge_libraries'
 include { MERGE_LIBRARIES as MERGE_LIBRARIES_GENOTYPING       } from '../subworkflows/local/merge_libraries'
 include { GENOTYPE                                            } from '../subworkflows/local/genotype'
@@ -594,8 +594,8 @@ workflow EAGER {
                 [ meta, vcf ]
             }
 
-        CLASSIFY_MTDNA_HAPLOGROUP(ch_mtdna_haplogroup_input)
-        ch_versions = ch_versions.mix(CLASSIFY_MTDNA_HAPLOGROUP.out.versions)
+        HAPLOTYPE_HUMAN_MTDNA(ch_mtdna_haplogroup_input)
+        ch_versions = ch_versions.mix(HAPLOTYPE_HUMAN_MTDNA.out.versions)
     }
 
     //