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| author | Justin Bedo <cu@cua0.org> | 2019-01-10 07:43:04 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-01-10 07:43:04 +1100 |
| commit | c6ea8db2830f99195cc74bc3e59992324a8c0480 (patch) | |
| tree | e0af4efeaebdf45affdcdae3ef524c29b3911def | |
| parent | c3babc9eb65dc8c56d07ce8a6ee0d8c03bbd223e (diff) | |
refactor missed stages
| -rw-r--r-- | tools/samtools-sort.nix | 2 | ||||
| -rw-r--r-- | tools/strelka-call.nix | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix index 6f9eb33..d01c83f 100644 --- a/tools/samtools-sort.nix +++ b/tools/samtools-sort.nix @@ -19,7 +19,7 @@ let outfmtR = if outfmt != null then outfmt input else input.filetype; outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;}; alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; none = _: false;} input; -in pkgs.stdenv.mkDerivation { +in stage { name = "samtools-sort"; buildInputs = with pkgs; [ samtools ]; buildCommand = diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index 95ce0f6..8505302 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -21,7 +21,7 @@ in assert (length (unique refs) == 1); -pkgs.stdenv.mkDerivation { +stage { name = "strelka"; buildInputs = with pkgs; [ strelka ]; buildCommand = '' |