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|
{ bionix
, ref
, bamOutput ? true
, flags ? null
, indexAttrs ? { }
}:
{ input1
, input2 ? null
}:
with bionix;
with lib;
with types;
with compression;
let
fa = f: matchFiletype "hisat2-ref" { fa = _: f; } f;
fq = f: matchFiletype "hisat2-input" { fq = _: f; gz = matchFiletype' "hisat2-input" { fq = _: "<(gunzip < ${f})"; }; } f;
in
stage {
name = "hisat2-align";
buildInputs = with pkgs; [ hisat2 bc samtools ];
buildCommand = ''
ln -s ${fa ref} ref.fa
cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
if [[ $cores -lt 1 ]] ; then
cores=1
fi
hisat2 ${optionalString (flags != null) flags} -p $cores -x ${hisat2.index indexAttrs ref}/index \
${if input2 != null then "-1 ${fq input1} -2 ${fq input2}" else "-U ${fq input1}"} \
${optionalString bamOutput "| samtools view -b"} \
| samtools sort -n \
> $out
'';
passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
passthru.multicore = true;
stripStorePaths = !bamOutput;
}
|
