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| author | Justin Bedo <cu@cua0.org> | 2020-04-27 09:46:48 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-04-27 09:46:48 +1000 |
| commit | dbe76116e2fa84e22740b139a1eab8217f130856 (patch) | |
| tree | 2faf21043ce646471a6fda6aad3c1ebb11439427 /tools | |
| parent | 98501e58830a93b531a1a5a172d666e66e6b4a6a (diff) | |
octopus: parameterise max-genotypes and targets
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/octopus-call.nix | 12 | ||||
| -rw-r--r-- | tools/octopus-callSomatic.nix | 11 |
2 files changed, 23 insertions, 0 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix index 57dd71f..ca0677e 100644 --- a/tools/octopus-call.nix +++ b/tools/octopus-call.nix @@ -1,8 +1,15 @@ { bionix +, fast ? false +, very-fast ? false +, max-genotypes ? null +, targets ? null , faidxAttrs ? {} , indexAttrs ? {} , flags ? ""}: +assert !fast || !very-fast; +assert max-genotypes == null || max-genotypes > 0; + with bionix; with lib; with types; @@ -30,6 +37,11 @@ stage { '') inputs} octopus -R ref.fa -I *.bam -o $out \ --threads=$NIX_BUILD_CORES \ + ${optionalString fast "--fast"} \ + ${optionalString very-fast "--very-fast"} \ + ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \ + ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \ + -N $normal \ ${flags} ''; passthru.filetype = filetype.vcf {ref = ref;}; diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix index e1c7ce6..5c2ca90 100644 --- a/tools/octopus-callSomatic.nix +++ b/tools/octopus-callSomatic.nix @@ -1,8 +1,15 @@ { bionix +, fast ? false +, very-fast ? false +, max-genotypes ? null +, targets ? null , faidxAttrs ? {} , indexAttrs ? {} , flags ? ""}: +assert !fast || !very-fast; +assert max-genotypes == null || max-genotypes > 0; + with bionix; with lib; with types; @@ -45,6 +52,10 @@ stage { normal=$(samtools view -H ${normal} | awk -f ${smScript}) octopus -R ref.fa -I *.bam -o $out \ --threads=$NIX_BUILD_CORES \ + ${optionalString fast "--fast"} \ + ${optionalString very-fast "--very-fast"} \ + ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \ + ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \ -N $normal \ ${flags} ''; |