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authorJustin Bedo <cu@cua0.org>2020-06-27 14:35:30 +1000
committerJustin Bedo <cu@cua0.org>2020-06-27 14:35:30 +1000
commit7611c8798f41427c5b48a3406d8bb9e0cde9786c (patch)
treeea23b6c68846e3428a37a4646507a4e95c3a91be
parent7e5542eadad1db9271fe1d18b5682eacebadbf48 (diff)
octopus: write evidence bams to multioutput
-rw-r--r--tools/octopus-call.nix3
-rw-r--r--tools/octopus-callSomatic.nix3
2 files changed, 6 insertions, 0 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 1688d88..f33d87c 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -28,6 +28,7 @@ assert (length (unique refs) == 1);
stage {
name = "octopus-call";
buildInputs = with pkgs; [ octopus-caller ];
+ outputs = [ "out" "evidence" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${samtools.faidx faidxAttrs ref} ref.fai
@@ -35,7 +36,9 @@ stage {
ln -s ${i} $(basename ${i}).bam
ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
'') inputs}
+ ${optionalString (length inputs > 1) "mkdir $evidence"}
octopus -R ref.fa -I *.bam -o $out \
+ --bamout $evidence \
--threads=$NIX_BUILD_CORES \
${optionalString fast "--fast"} \
${optionalString very-fast "--very-fast"} \
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index 5c2ca90..d3e7f96 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -42,6 +42,7 @@ assert (length (unique refs) == 1);
stage {
name = "octopus-callSomatic";
buildInputs = with pkgs; [ octopus-caller samtools ];
+ outputs = [ "out" "evidence" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${samtools.faidx faidxAttrs ref} ref.fai
@@ -50,7 +51,9 @@ stage {
ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
'') inputs}
normal=$(samtools view -H ${normal} | awk -f ${smScript})
+ mkdir $evidence
octopus -R ref.fa -I *.bam -o $out \
+ --bamout $evidence \
--threads=$NIX_BUILD_CORES \
${optionalString fast "--fast"} \
${optionalString very-fast "--very-fast"} \