diff options
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 = |