diff options
Diffstat (limited to 'tools/strelka-callSomatic.nix')
-rw-r--r-- | tools/strelka-callSomatic.nix | 28 |
1 files changed, 7 insertions, 21 deletions
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix index 888e589..6d379f9 100644 --- a/tools/strelka-callSomatic.nix +++ b/tools/strelka-callSomatic.nix @@ -17,14 +17,12 @@ let refs = map getref inputs; ref = head refs; - drv = bionix.strelka.callSomatic {inherit indexAttrs bamIndexAttrs flags;} {inherit normal tumour;}; - in assert (length (unique refs) == 1); stage { - name = "strelka-callSomatic"; + name = "strelka"; buildInputs = with pkgs; [ strelka gzip ]; buildCommand = '' ln -s ${ref} ref.fa @@ -33,27 +31,15 @@ stage { ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} configureStrelkaSomaticWorkflow.py \ - --normalBam ${filename normal}.bam \ - --tumourBam ${filename tumour}.bam \ - --ref ref.fa \ - --runDir $TMPDIR + --normalBam ${filename normal}.bam \ + --tumourBam ${filename tumour}.bam \ + --ref ref.fa \ + --runDir $TMPDIR ./runWorkflow.py \ - -m local \ - -j $NIX_BUILD_CORES + -m local \ + -j $NIX_BUILD_CORES cp -r results $out ''; - passthru = { - indels = stage { - name = "strelka-callVariants-indels"; - buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out"; - passthru.filetype = filetype.gz (filetype.vcf {ref = ref;}); - }; - snvs = stage { - name = "strelka-callVariants-snvs"; - buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out"; - passthru.filetype = filetype.gz (filetype.vcf {ref = ref;}); - }; - }; } |