diff options
Diffstat (limited to 'tools/bowtie-align.nix')
| -rw-r--r-- | tools/bowtie-align.nix | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix index 65d0e9f..57b0b01 100644 --- a/tools/bowtie-align.nix +++ b/tools/bowtie-align.nix @@ -20,7 +20,7 @@ let in stage { name = "bowtie2-align"; - buildInputs = with pkgs; [ bowtie2 bc ] ++ optional bamOutput samtools; + buildInputs = with pkgs; [ bowtie2 bc samtools ]; buildCommand = '' cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) if [[ $cores -lt 1 ]] ; then @@ -28,6 +28,7 @@ in stage { fi bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \ ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \ + | samtools sort -n \ ${optionalString bamOutput "| samtools view -b"} \ > $out ''; |