strelka: add germline calling

1 files changed, 3 insertions, 5 deletions

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 8505302..cbdcfb4 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -4,7 +4,7 @@
 , flags ? null
 }:
 
-{normal, tumour}:
+inputs:
 
 with bionix;
 with lib;
@@ -13,7 +13,6 @@ with types;
 let
   filename = path: last (splitString "/" path);
   getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
-  inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
 
@@ -30,9 +29,8 @@ stage {
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
-    configureStrelkaSomaticWorkflow.py \
-      --normalBam ${filename normal}.bam \
-      --tumourBam ${filename tumour}.bam \
+    configureStrelkaGermlineWorkflow.py \
+      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
       --ref ref.fa \
       --runDir $TMPDIR