fix: change bm names to adhere to naming scheme in pm4onco (#78)

* fix: change bm names to adhere to naming scheme in pm4onco

* fix: change bm name in test config

* fix: change seqc bm name in test config

---------

Co-authored-by: Bianca Stöcker <BiancaStoecker@users.noreply.github.com>

.test/config/config.yaml

@@ -7,11 +7,11 @@ variant-calls:
     benchmark: "chm-eval"
   dummy-imgag:
     path: "resources/variants/na12878-somatic/all.truth.bcf"
-    benchmark: "imgag-somatic-5perc"
+    benchmark: "imgag-5"
     tumor_sample_name: "HG001"
   dummy-seqc2:
     path: "resources/variants/seqc2-somatic/all.truth.format-added.vcf.gz"
-    benchmark: "seqc2-somatic-ea"
+    benchmark: "seqc2-wes"
     tumor_sample_name: "truth"
     vaf-field: 
       - INFO

workflow/resources/presets.yaml

@@ -10,7 +10,7 @@ benchmarks:
     bam-url: ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR134/ERR1341796/CHM1_CHM13_2.bam
     grch37: false
 
-  seqc2-somatic-ea:
+  seqc2-wes:
     genome: seqc2-somatic
     bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/WES/WES_EA_T_1.bwa.dedup.bam
     target-regions: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/technical/reference_genome/Exome_Target_bed/S07604624_Covered_human_all_v6_plus_UTR.liftover.to.hg38.bed6.gz
@@ -20,28 +20,28 @@ benchmarks:
       - TVAF # name of tumor variant allele frequency
     high-coverage: true
 
-  imgag-somatic-5perc:
+  imgag-5:
     genome: na12878-somatic
     bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_5.bam
     target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
     grch37: false
     high-coverage: true
 
-  imgag-somatic-10perc:
+  imgag-10:
     genome: na12878-somatic
     bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_10.bam
     target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
     grch37: false
     high-coverage: true
 
-  imgag-somatic-20perc:
+  imgag-20:
     genome: na12878-somatic
     bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_20.bam
     target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
     grch37: false
     high-coverage: true
 
-  imgag-somatic-40perc:
+  imgag-40:
     genome: na12878-somatic
     bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_40.bam
     target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed