Merge branch 'master' of https://github.com/PapenfussLab/bionix

1 files changed, 6 insertions, 4 deletions

diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index 54edc85..b50a01c 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -5,6 +5,7 @@
 , flags ? null
 , unmappedReads ? false
 , minClipLength ? 5
+, collectMetricsAttrs ? {}
 , config ? null
 }:
 
@@ -27,16 +28,17 @@ stdenv.mkDerivation rec {
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     ln -s ${bionix.samtools.dict dictIndexAttrs ref} ref.fa.dict
     ln -s ${input} input.bam
-    mkdir $out
+    for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do
+      ln -s $f
+    done
     java -Dsamjdk.create_index=true \
       -cp ${bionix.gridss.jar} gridss.ExtractSVReads \
       REFERENCE_SEQUENCE=ref.fa \
       I=input.bam \
-      O=$out/input.sv.bam \
-      METRICS_OUTPUT=$out/input.sv_metrics \
-      INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
+      O=$out \
       UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
       ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
       MIN_CLIP_LENGTH=${toString minClipLength}
   '';
+  passthru.filetype = input.filetype;
 }