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| author | Justin Bedo <cu@cua0.org> | 2018-11-22 10:43:54 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-22 10:43:54 +1100 |
| commit | 24ee2349c16f159f2627665938fd76d599055a9a (patch) | |
| tree | 54a5bce88dc1403f67f58457c2b27882bc32d193 /tools/gridss-identifyVariants.nix | |
| parent | 90dd48b019ff7bf9e74d202c1deace6a0896cde5 (diff) | |
gridss: fix configure file optional string error
Diffstat (limited to 'tools/gridss-identifyVariants.nix')
| -rw-r--r-- | tools/gridss-identifyVariants.nix | 10 |
1 files changed, 4 insertions, 6 deletions
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix index 16982e2..c91de00 100644 --- a/tools/gridss-identifyVariants.nix +++ b/tools/gridss-identifyVariants.nix @@ -42,26 +42,24 @@ assert (homoRef); stdenv.mkDerivation rec { name = "gridss-identifyVariants"; - buildInputs = [ jre ]; + buildInputs = [ jre samtools ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do ln -s $f done - ${concatMapStringsSep "\n" (linkInput extractSVReads extractSVReadsAttrs) inputs} + ${concatMapStringsSep "\n" (linkSV) inputs} + ${linkSV assembly} ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs} ${linkInput collectMetrics collectMetricsAttrs assembly} - ASSBASE=$(basename ${assembly}) - ln -s ${assembly} $ASSBASE.gridss.working/$ASSBASE.sv.bam - ln -s ${bionix.samtools.index {} assembly} $ASSBASE.gridss.working/$ASSBASE.sv.bai java -Xmx4g -Dsamjdk.create_index=true \ -cp ${jar} gridss.IdentifyVariants \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ OUTPUT_VCF=out.vcf \ - ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ |