diff options
Diffstat (limited to 'tools/gridss-variants.nix')
-rw-r--r-- | tools/gridss-variants.nix | 24 |
1 files changed, 16 insertions, 8 deletions
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index a5c470a..62a89f6 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -1,7 +1,14 @@ -{ bionix, bwaIndexAttrs ? { }, faidxAttrs ? { }, indexAttrs ? { } -, assemblyAttrs ? { }, collectMetricsAttrs ? { } +{ bionix +, bwaIndexAttrs ? { } +, faidxAttrs ? { } +, indexAttrs ? { } +, assemblyAttrs ? { } +, collectMetricsAttrs ? { } , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } -, config ? null, heapSize ? "4g", shards ? 10 }: +, config ? null +, heapSize ? "4g" +, shards ? 10 +}: with bionix; with lib; @@ -47,15 +54,16 @@ let for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do ln -s $f done - ${concatMapStringsSep "\n" (linkSV) inputs} + ${concatMapStringsSep "\n" linkSV inputs} ${linkSV assembly} ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs} ${linkInput collectMetrics collectMetricsAttrs assembly} ''; -in assert (all sorted inputs); -assert (homoRef); +in +assert (all sorted inputs); +assert homoRef; rec { identify = stage rec { @@ -80,7 +88,7 @@ rec { mv out.vcf $out ''; passthru = { - filetype = filetype.vcf { ref = ref; }; + filetype = filetype.vcf { inherit ref; }; gridss.assembly = assembly; multicore = true; }; @@ -115,7 +123,7 @@ rec { mv out.vcf $out ''; passthru = { - filetype = filetype.vcf { ref = ref; }; + filetype = filetype.vcf { inherit ref; }; gridss.assembly = assembly; multicore = true; }; |