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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 "star-ref" { fa = _: f; } f;
fq = f: matchFiletype "star-input" { fq = _: f; gz = matchFiletype' "star-input" { fq = _: "<(gunzip < ${f})"; }; } f;
in stage {
name = "star-align";
buildInputs = with pkgs; [ star 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
STAR ${optionalString (flags != null) flags} \
--runThreadN $cores \
--genomeDir ${star.index indexAttrs ref} \
--readFilesIn ${fq input1} ${optionalString (input2 != null) (fq input2)}
${if bamOutput then "samtools view -b Aligned.out.sam > $out" else "cp Aligned.out.sam $out"}
'';
passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
passthru.multicore = true;
}
|
