diff options
Diffstat (limited to 'tools/gridss-extractSVReads.nix')
| -rw-r--r-- | tools/gridss-extractSVReads.nix | 11 |
1 files changed, 6 insertions, 5 deletions
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index e3ed1cc..b5ceffb 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -27,16 +27,17 @@ 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \ MIN_CLIP_LENGTH=${toString minClipLength} ''; + passthru.filetype = input.filetype; } |