From ab809b8c77efdad9fb54d3591a0193a1cbe888d1 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 29 Oct 2021 15:27:22 +1100
Subject: octopus: write region lists to region files

---
 tools/octopus-call.nix        | 29 +++++++++++++++++++++++------
 tools/octopus-callSomatic.nix | 31 +++++++++++++++++++++++--------
 2 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index f33d87c..80092e0 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -3,9 +3,10 @@
 , very-fast ? false
 , max-genotypes ? null
 , targets ? null
-, faidxAttrs ? {}
-, indexAttrs ? {}
-, flags ? ""}:
+, faidxAttrs ? { }
+, indexAttrs ? { }
+, flags ? ""
+}:
 
 assert !fast || !very-fast;
 assert max-genotypes == null || max-genotypes > 0;
@@ -17,10 +18,26 @@ with types;
 inputs:
 
 let
-  getref = f: matchFiletype "octopus-call" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
+  getref = f: matchFiletype "octopus-call" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; } f;
   refs = map getref inputs;
   ref = head refs;
 
+
+  handleTarget = x:
+    let
+      type = builtins.typeOf x;
+      handler = handlers."${type}" or (builtins.throw "octopus-callSomatic:unhandled target type:${type}");
+      handlers = {
+        string = "-T '${x}'";
+        list =
+          let file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
+          in "-t ${file}";
+        path = "-t ${x}";
+      };
+    in
+    handler;
+
+
 in
 
 assert (length (unique refs) == 1);
@@ -43,9 +60,9 @@ stage {
       ${optionalString fast "--fast"} \
       ${optionalString very-fast "--very-fast"} \
       ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
-      ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
+      ${optionalString (targets != null) (handleTarget targets)} \
       ${flags}
   '';
-  passthru.filetype = filetype.vcf {ref = ref;};
+  passthru.filetype = filetype.vcf { ref = ref; };
   passthru.multicore = true;
 }
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index d3e7f96..401eeb8 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -3,9 +3,10 @@
 , very-fast ? false
 , max-genotypes ? null
 , targets ? null
-, faidxAttrs ? {}
-, indexAttrs ? {}
-, flags ? ""}:
+, faidxAttrs ? { }
+, indexAttrs ? { }
+, flags ? ""
+}:
 
 assert !fast || !very-fast;
 assert max-genotypes == null || max-genotypes > 0;
@@ -14,7 +15,7 @@ with bionix;
 with lib;
 with types;
 
-{normal, tumours}:
+{ normal, tumours }:
 
 let
   smScript = pkgs.writeText "smScript.awk" ''
@@ -29,11 +30,25 @@ let
     }
   '';
 
-  inputs = [normal] ++ tumours;
-  getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
+  inputs = [ normal ] ++ tumours;
+  getref = f: matchFiletype "octopus-callSomatic" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; } f;
   refs = map getref inputs;
   ref = head refs;
 
+  handleTarget = x:
+    let
+      type = builtins.typeOf x;
+      handler = handlers."${type}" or (builtins.throw "octopus-callSomatic:unhandled target type:${type}");
+      handlers = {
+        string = "-T '${x}'";
+        list =
+          let file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
+          in "-t ${file}";
+        path = "-t ${x}";
+      };
+    in
+    handler;
+
 in
 
 assert (length (unique refs) == 1);
@@ -58,10 +73,10 @@ stage {
       ${optionalString fast "--fast"} \
       ${optionalString very-fast "--very-fast"} \
       ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
-      ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
+      ${optionalString (targets != null) (handleTarget targets)} \
       -N $normal \
       ${flags}
   '';
-  passthru.filetype = filetype.vcf {ref = ref;};
+  passthru.filetype = filetype.vcf { ref = ref; };
   passthru.multicore = true;
 }
-- 
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