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/bowtie-align.nix | |
parent | ab809b8c77efdad9fb54d3591a0193a1cbe888d1 (diff) |
treewide reformatting and simplification
- simplify with statix
- reformat with nixpkgs-fmt
Diffstat (limited to 'tools/bowtie-align.nix')
-rw-r--r-- | tools/bowtie-align.nix | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix index c83c49c..8df3dba 100644 --- a/tools/bowtie-align.nix +++ b/tools/bowtie-align.nix @@ -2,7 +2,7 @@ , ref , bamOutput ? true , flags ? null -, indexAttrs ? {} +, indexAttrs ? { } }: { input1 @@ -18,7 +18,8 @@ let fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f; fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f; -in stage { +in +stage { name = "bowtie2-align"; buildInputs = with pkgs; [ bowtie2 bc samtools ]; buildCommand = '' @@ -32,6 +33,6 @@ in stage { ${optionalString bamOutput "| samtools view -b"} \ > $out ''; - passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};}; + passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; } |