From 6137d292d8d721490bf6ded2695cdc71755aff59 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 9 May 2019 14:23:53 +1000
Subject: strelka: rewrite to use multiple outputs
---
tools/strelka-call.nix | 10 ++++++++--
tools/strelka-callSomatic.nix | 13 +++++++++++--
tools/strelka.nix | 32 --------------------------------
3 files changed, 19 insertions(+), 36 deletions(-)
(limited to 'tools')
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index bc1e202..dc07291 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -20,9 +20,11 @@ in
assert (length (unique refs) == 1);
-stage {
+let
+out = stage {
name = "strelka-call";
buildInputs = with pkgs; [ strelka ];
+ outputs = [ "out" "variants" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -48,8 +50,12 @@ stage {
sed -i '/^##fileDate/d' $g
sed -i '/^##startTime/d' $g
done
+ mv variants.vcf $variants
+ ln -s $variants variants.vcf
mkdir $out
cp -r * $out
'';
passthru.multicore = true;
-}
+};
+ft = {filetype = types.filetype.vcf {ref = ref;};};
+in out // { variants = out.variants // ft; }
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index cf4b414..cce6243 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -21,9 +21,12 @@ in
assert (length (unique refs) == 1);
-stage {
+let
+
+out = stage {
name = "strelka-callSomatic";
buildInputs = with pkgs; [ strelka ];
+ outputs = [ "out" "indels" "snvs" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -50,8 +53,14 @@ stage {
sed -i '/^##fileDate/d' $g
sed -i '/^##startTime/d' $g
done
+ mv somatic.indels.vcf $indels
+ ln -s $indels somatic.indels.vcf
+ mv somatic.snvs.vcf $snvs
+ ln -s $snvs somatic.snvs.vcf
mkdir $out
cp -r * $out
'';
passthru.multicore = true;
-}
+};
+ft = {filetype = types.filetype.vcf {ref = ref;};};
+in out // { indels = out.indels // ft; snvs = out.snvs // ft;}
diff --git a/tools/strelka.nix b/tools/strelka.nix
index d3068b5..16f4a2b 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -12,36 +12,4 @@ with types;
Type: call :: {...} -> [input] -> results
*/
call = callBionixE ./strelka-call.nix;
- /* Extract VCF file from results
- Type: variants :: results -> vcf
- */
- variants =
- # result of call
- drv: stage {
- name = "strelka-call-variants";
- buildCommand = ''
- ln -s ${drv}/variants/variants.vcf $out
- '';
- passthru.filetype = filetype.vcf {ref=ref;};
- };
- /* Extract indels from somatic results
- Type: indels :: somatic results -> vcf
- */
- indels =
- # result of callSomatic
- drv: stage {
- name = "strelka-callVariants-indels";
- buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf $out";
- passthru.filetype = filetype.vcf {ref = ref;};
- };
- /* Extract SNVs from somatic results
- Type: snvs :: somatic results -> vcf
- */
- snvs =
- # result of callSomatic
- drv: stage {
- name = "strelka-callVariants-snvs";
- buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf $out";
- passthru.filetype = filetype.vcf {ref = ref;};
- };
}
--
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