Merge pull request #366 from genomic-medicine-sweden/Smeds-patch-1

fix: clean config file
genomic-medicine-sweden · Nov 15, 2023 · 5b020bf · 5b020bf
2 parents 1c77dad + 7b908df
commit 5b020bf
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Showing 3 changed files with 14 additions and 16 deletions.
diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml
@@ -109,6 +109,11 @@ hotspot_report:
 manta_config_t:
   extra: "--exome --callRegions {{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz"
 
+merge_cnv_json:
+  annotations:
+    - {{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes.bed
+    - {{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed
+
 mosdepth:
   extra: "--no-per-base --fast-mode"
 

diff --git a/config/config.yaml b/config/config.yaml
@@ -14,9 +14,6 @@ arriba:
 
 arriba_draw_fusion:
   container: "docker://hydragenetics/arriba:2.3.0"
-  cytobands: "/data/ref_data/arriba/arriba_v2.3.0/database/cytobands_hg19_hs37d5_GRCh37_v2.3.0.tsv"
-  gtf: "/data/ref_genomes/hg19/gtf/hg19.refGene.gtf"
-  protein_domains: "/data/ref_data/arriba/arriba_v2.3.0/database/protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3"
 
 add_multi_snv_in_codon:
   af_limit: 0.00
@@ -185,9 +182,6 @@ manta_run_workflow_t:
   container: "docker://hydragenetics/manta:1.6.0"
 
 merge_cnv_json:
-  annotations:
-    - /projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/bed/cnv_amp_genes.bed
-    - /projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/bed/cnv_loh_genes.bed
   filtered_cnv_vcfs:
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.filter.cnv_hard_filter_amp.vcf.gz
     - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.filter.cnv_hard_filter_loh.vcf.gz
@@ -369,7 +363,6 @@ vardict:
 
 vep:
   container: "docker://hydragenetics/vep:105"
-  vep_cache:  "/data/ref_genomes/VEP/"
   mode: --offline --cache --refseq
   extra: " --assembly GRCh37 --check_existing --pick --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
 

diff --git a/config/references/design_files.hg19.yaml b/config/references/design_files.hg19.yaml
@@ -97,24 +97,24 @@
 
  hotspot_annotation:
    hotspots:
-     checksum: 59fe5daf8039746c6690fce5e55d5115
-     path: GMS560/reports/Hotspots_combined_regions_nodups.csv
+     checksum: 50564a9b99f86b123bb61f6e361eff10
+     path: GMS560/reports/Hotspots_combined_regions_nodups.231011.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/design/Hotspots_combined_regions_nodups.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.3.0/design/Hotspots_combined_regions_nodups.231011.csv
 
  hotspot_info:
    hotspot_mutations:
-     checksum: 59fe5daf8039746c6690fce5e55d5115
-     path: GMS560/reports/Hotspots_combined_regions_nodups.csv
+     checksum: 50564a9b99f86b123bb61f6e361eff10
+     path: GMS560/reports/Hotspots_combined_regions_nodups.231011.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/design/Hotspots_combined_regions_nodups.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.3.0/design/Hotspots_combined_regions_nodups.231011.csv
 
  hotspot_report:
    hotspot_mutations:
-     checksum: 59fe5daf8039746c6690fce5e55d5115
-     path: GMS560/reports/Hotspots_combined_regions_nodups.csv
+     checksum: 50564a9b99f86b123bb61f6e361eff10
+     path: GMS560/reports/Hotspots_combined_regions_nodups.231011.csv
      type: file
-     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/design/Hotspots_combined_regions_nodups.csv
+     url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.0.0/design/Hotspots_combined_regions_nodups.231011.csv
 
  manta_config_t:
    extra: