diff options
author | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
commit | bac9248a5e08e8afdf5485a6e27cfe72e1ca5090 (patch) | |
tree | 8719a280b56122017d46b582cd3da8547dd3f548 /tools/samtools-sort.nix | |
parent | ab809b8c77efdad9fb54d3591a0193a1cbe888d1 (diff) |
treewide reformatting and simplification
- simplify with statix
- reformat with nixpkgs-fmt
Diffstat (limited to 'tools/samtools-sort.nix')
-rw-r--r-- | tools/samtools-sort.nix | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix index e3fbff8..30439f1 100644 --- a/tools/samtools-sort.nix +++ b/tools/samtools-sort.nix @@ -17,9 +17,10 @@ assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: 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 stage { + 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 +stage { name = "samtools-sort"; buildInputs = with pkgs; [ samtools ]; buildCommand = |