diff options
Diffstat (limited to 'tools/gridss-callVariants.nix')
| -rw-r--r-- | tools/gridss-callVariants.nix | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index f42e3f3..ad659de 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -1,7 +1,7 @@ { bionix , blacklist ? null -, bwaIndexAttrs ? {} -, faidxAttrs ? {} +, bwaIndexAttrs ? { } +, faidxAttrs ? { } , flags ? null , config ? null , heapSize ? "31g" @@ -32,22 +32,22 @@ stage rec { done mkdir $out java -ea -Xmx${heapSize} \ - -Dreference_fasta="ref.fa" \ - -Dsamjdk.create_index=true \ - -Dsamjdk.use_async_io_read_samtools=true \ - -Dsamjdk.use_async_io_write_samtools=true \ - -Dsamjdk.use_async_io_write_tribble=true \ - -Dgridss.gridss.output_to_temp_file=true \ - -cp ${bionix.gridss.jar} gridss.CallVariants \ + -Dreference_fasta="ref.fa" \ + -Dsamjdk.create_index=true \ + -Dsamjdk.use_async_io_read_samtools=true \ + -Dsamjdk.use_async_io_write_samtools=true \ + -Dsamjdk.use_async_io_write_tribble=true \ + -Dgridss.gridss.output_to_temp_file=true \ + -cp ${bionix.gridss.jar} gridss.CallVariants \ VERBOSITY=WARNING \ WORKER_THREADS=$NIX_BUILD_CORES \ - TMP_DIR=. \ - WORKING_DIR=. \ + TMP_DIR=. \ + WORKING_DIR=. \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ - REFERENCE_SEQUENCE="ref.fa" \ + REFERENCE_SEQUENCE="ref.fa" \ ${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \ - OUTPUT="$out/gridss.vcf" \ - ASSEMBLY="$out/gridss.bam" \ + OUTPUT="$out/gridss.vcf" \ + ASSEMBLY="$out/gridss.bam" \ ${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \ ${optionalString (flags != null) flags} |