refactor: update all output with normalizre etc

clinical-genomics-uppsala · Nov 5, 2024 · 56ebffa · 56ebffa
1 parent 65c4786
commit 56ebffa
Showing 1 changed file with 37 additions and 37 deletions.
diff --git a/config/output_files.yaml b/config/output_files.yaml
@@ -24,55 +24,55 @@ files:
   # Tumor
     # SNV indels
   - name: Parabricks T vcf
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_T.vep.vcf.gz"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.vcf.gz"
     types: ["T"]
 
   - name: Parabricks T tbi
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_T.vep.vcf.gz.tbi"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.vcf.gz.tbi"
     types: ["T"]
 
   - name: Parabricks T vcf ALL subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.all.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_T.vep.all.vcf.gz" 
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.all.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.all.vcf.gz"
     types: ["T"]
 
   - name: Parabricks T tbi ALL subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.all.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_T.vep.all.vcf.gz.tbi"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.all.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.all.vcf.gz.tbi"
     types: ["T"]
 
   - name: Parabricks T vcf AML subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.aml.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_T.vep.aml.vcf.gz"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.aml.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.aml.vcf.gz"
     types: ["T"]
 
   - name: Parabricks T tbi AML subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.aml.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_T.vep.aml.vcf.gz.tbi"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.aml.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.aml.vcf.gz.tbi"
     types: ["T"]
 
   - name: Parabricks T vcf TM subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.tm.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_T.vep.tm.vcf.gz"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.tm.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.tm.vcf.gz"
     types: ["T"]  
 
   - name: Parabricks T tbi TM subsample
-    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.vep.include.tm.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_T.vep.tm.vcf.gz.tbi"
-    types: ["T"]
-
-  - name: Parabricks T xlsx
-    input: "export_to_xlsx/t/{sample}_T.snvs.xlsx"
-    output: "{sample}/SNV_indels/{sample}_T.xlsx"
+    input: "parabricks/pbrun_mutectcaller_t/{sample}_T.normalized.vep.ratio.filter.somatic.include.tm.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_T.normalized.vep.ratio.filter.somatic.tm.vcf.gz.tbi"
     types: ["T"]
 
   - name: Pindel vcf
     input: "cnv_sv/pindel_vcf/{sample}_T.no_tc.vep_annotated.vcf"
     output: "{sample}/SNV_indels/{sample}.pindel.vcf"
     types: ["T"]
 
+  - name: Parabricks T xlsx
+    input: "export_to_xlsx/t/{sample}_T.snvs.xlsx"
+    output: "{sample}/SNV_indels/{sample}_T.xlsx"
+    types: ["T"]
+
     # CNV
   - name: CNVkit vcf
     input: "cnv_sv/cnvkit_vcf/{sample}_T.pathology.vcf.gz"
@@ -199,43 +199,43 @@ files:
   # Matched samples TN
     # SNV indels
   - name: Parabricks TN vcf
-    input: "parabricks/pbrun_mutectcaller_tn/{sample}.vep.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_TN.vep.vcf.gz"
+    input: "parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.vcf.gz"
     types:  ["TN"]
 
   - name: Parabricks TN tbi
-    input: "parabricks/pbrun_mutectcaller_tn/{sample}.vep.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_TN.vep.vcf.gz.tbi"
+    input: "parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.vcf.gz.tbi"
     types:  ["TN"]
 
   - name: Parabricks TN vcf ALL subsample
-    input: "parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.all.vcf.gz"
-    output: "{sample}/SNV_indels/{sample}_TN.vep.all.vcf.gz"
+    input: "parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.all.vcf.gz"
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.all.vcf.gz"
     types: ["TN"]
 
   - name: Parabricks TN tbi ALL subsample
-    input: "parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.all.vcf.gz.tbi"
-    output: "{sample}/SNV_indels/{sample}_TN.vep.all.vcf.gz.tbi"
+    input: "parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.all.vcf.gz.tbi"
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.all.vcf.gz.tbi"
     types: ["TN"]
 
   - name: Parabricks TN vcf AML subsample
-    input: parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.aml.vcf.gz
-    output: "{sample}/SNV_indels/{sample}_TN.vep.aml.vcf.gz"
+    input: parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.aml.vcf.gz
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.aml.vcf.gz"
     types: ["TN"]
 
   - name: Parabricks TN tbi AML subsample
-    input: parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.aml.vcf.gz.tbi
-    output: "{sample}/SNV_indels/{sample}_TN.vep.aml.vcf.gz.tbi"
+    input: parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.aml.vcf.gz.tbi
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.aml.vcf.gz.tbi"
     types: ["TN"]
 
   - name: Parabricks TN vcf TM subsample
-    input: parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.tm.vcf.gz
-    output: "{sample}/SNV_indels/{sample}_TN.vep.tm.vcf.gz"
+    input: parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.tm.vcf.gz
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.tm.vcf.gz"
     types: ["TN"]
 
   - name: Parabricks TN tbi TM subsample
-    input: parabricks/pbrun_mutectcaller_tn/{sample}.vep.include.tm.vcf.gz.tbi
-    output: "{sample}/SNV_indels/{sample}_TN.vep.tm.vcf.gz.tbi"
+    input: parabricks/pbrun_mutectcaller_tn/{sample}.normalized.vep.ratio.filter.somatic.include.tm.vcf.gz.tbi
+    output: "{sample}/SNV_indels/{sample}_TN.normalized.vep.ratio.filter.somatic.tm.vcf.gz.tbi"
     types: ["TN"]
 
   - name: Parabricks TN xlsx