Rename to CLASSIFY_MTDNA_HAPLOGROUP

Author: VerbalCant

conf/modules.config

@@ -1863,7 +1863,7 @@ process {
 
     // This should not be here. We should pass it in as an argument to the subworkflow, but I'm
     // still figuring out how to do that.
-    withName: 'NFCORE_EAGER:EAGER:HAPLOTYPE_HUMAN_MTDNA:HAPLOGREP3_CLASSIFY' {
+    withName: 'NFCORE_EAGER:EAGER:CLASSIFY_MTDNA_HAPLOGROUP:HAPLOGREP3_CLASSIFY' {
         ext.args = '--tree phylotree-fu-rcrs@1.2'
     }
 }

docs/development/manual_tests.md

@@ -1136,6 +1136,8 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ --convert_
 
 ### MTDNA HAPLOGROUP CLASSIFICATION
 
+#### ALAINA TODO: ADD SOMETHING HERE
+
 ```bash
 #### MTDNA HAPLOGROUP CLASSIFICATION with default settings
 ## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
@@ -1146,10 +1148,4 @@ nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_te
 ## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
 ## Expect: The haplogroup assignment may differ based on the classification settings
 nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test_args --run_mtdna_haplogroup --haplogrep_args '--extend-report' -resume
-
-#### MTDNA HAPLOGROUP CLASSIFICATION with custom VCF input
-## Use as input a version of the TSV that contains mitochondrial VCF files
-## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
-## Expect: The haplogroup assignment should reflect the variants in the input VCF files
-nextflow run main.nf -profile docker,test --input ~/eager_dsl2_testing/input/mtdna/mtdna_vcf_samples.tsv --outdir ./results/mtdna_haplogroup_vcf_test --run_mtdna_haplogroup -resume
 ```

…workflows/local/haplotype_human_mtdna.nf …flows/local/classify_mtdna_haplogroup.nfsubworkflows/local/haplotype_human_mtdna.nf renamed to subworkflows/local/classify_mtdna_haplogroup.nf subworkflows/local/haplotype_human_mtdna.nf renamed to subworkflows/local/classify_mtdna_haplogroup.nf

@@ -7,7 +7,7 @@
 include { addNewMetaFromAttributes      } from '../../subworkflows/local/utils_nfcore_eager_pipeline/main'
 include { HAPLOGREP3_CLASSIFY           } from '../../modules/nf-core/haplogrep3/classify/main'
 
-workflow HAPLOTYPE_HUMAN_MTDNA {
+workflow CLASSIFY_MTDNA_HAPLOGROUP {
 
     take:
     ch_mtdna_vcf

workflows/eager.nf

@@ -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 { HAPLOTYPE_HUMAN_MTDNA                               } from '../subworkflows/local/haplotype_human_mtdna'
+include { CLASSIFY_MTDNA_HAPLOGROUP                          } from '../subworkflows/local/classify_mtdna_haplogroup'
 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'
@@ -586,8 +586,8 @@ workflow EAGER {
                 [ meta, vcf ]
             }
 
-        HAPLOTYPE_HUMAN_MTDNA(ch_mtdna_haplogroup_input)
-        ch_versions = ch_versions.mix(HAPLOTYPE_HUMAN_MTDNA.out.versions)
+        CLASSIFY_MTDNA_HAPLOGROUP(ch_mtdna_haplogroup_input)
+        ch_versions = ch_versions.mix(CLASSIFY_MTDNA_HAPLOGROUP.out.versions)
     }
 
     //