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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-10-24 21:53:56 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-10-24 21:53:56 +1100 |
| commit | 7daac8bb4bd0d705662c18b677a69d3785f4d8f8 (patch) | |
| tree | 43ae4be3ec4418190c3fabff312cdce7c10868b3 /tools | |
| parent | fdcf948c93ee5a3a3f00e38f5d4fed7bc964a56b (diff) | |
| parent | e25bd63e03ee4da6817fe437e5e4184eae685653 (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/bwa-mem.nix | 3 | ||||
| -rw-r--r-- | tools/platypus-callVariants.nix | 2 |
2 files changed, 2 insertions, 3 deletions
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 0d0f7d8..3208e48 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -29,8 +29,7 @@ in stdenv.mkDerivation { done cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) if [[ $cores -lt 1 ]] ; then - >&2 echo "not enough build cores" - exit 1 + cores=1 fi bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \ ${optionalString (input2 != null) (fq input2)} \ diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix index a3e3a65..a57aa83 100644 --- a/tools/platypus-callVariants.nix +++ b/tools/platypus-callVariants.nix @@ -14,7 +14,7 @@ with bionix.types; let filename = path: last (splitString "/" path); - getref = f: matchFiletype "platypus-callVariants" { bam = r: r; } f; + getref = f: matchFiletype "platypus-callVariants" { bam = {ref, ...}: ref; } f; refs = map getref inputs; ref = head refs; in |