refactor: use named input for svdb merge

clinical-genomics-uppsala · Apr 16, 2024 · 198f8f8 · 198f8f8
1 parent 615027d
commit 198f8f8
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Showing 2 changed files with 6 additions and 8 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -186,11 +186,9 @@ use rule smn_manifest from cnv_sv as cnv_sv_smn_manifest with:
 
 use rule svdb_merge from cnv_sv as cnv_sv_svdb_merge with:
     input:
-        vcfs=[
-            "cnv_sv/tiddit/{sample}_{type}.vcf",
-            "cnv_sv/manta_run_workflow_n/{sample}/results/variants/diploidSV.vcf.gz",
-            "cnv_sv/cnvpytor/{sample}_{type}.softfiltered.vcf",
-        ],
+        tiddit="cnv_sv/tiddit/{sample}_{type}.vcf",
+        manta="cnv_sv/manta_run_workflow_n/{sample}/results/variants/diploidSV.vcf.gz",
+        cnvpytor="cnv_sv/cnvpytor/{sample}_{type}.softfiltered.vcf",
     output:
         vcf=temp("cnv_sv/svdb_merge/{sample}_{type}.merged.vcf"),
     params:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -228,9 +228,9 @@ def get_glnexus_input(wildcards, input):
 
 def get_vcfs_for_svdb_merge(wildcards, input):
     vcfs_with_suffix = []
-    for v in input.vcfs:
-        caller = os.path.dirname(v).split("/")[1].split("_")[0]
-        vcfs_with_suffix.append(f"{v}:{caller}")
+    vcfs_with_suffix.append(f"{input.tiddit}:tiddit")
+    vcfs_with_suffix.append(f"{input.manta}:manta")
+    vcfs_with_suffix.append(f"{input.cnvpytor}:cnvpytor")
 
     return vcfs_with_suffix