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|
{ bionix
, indexAttrs ? {}
, bamIndexAttrs ? {}
, flags ? null
}:
inputs:
with bionix;
with lib;
with types;
let
filename = path: last (splitString "/" path);
getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
refs = map getref inputs;
ref = head refs;
drv = bionix.strelka.call {inherit indexAttrs bamIndexAttrs flags;} inputs;
in
assert (length (unique refs) == 1);
stage {
name = "strelka-call";
buildInputs = with pkgs; [ strelka ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
configureStrelkaGermlineWorkflow.py \
${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
--ref ref.fa \
--runDir $TMPDIR
./runWorkflow.py \
-m local \
-j $NIX_BUILD_CORES 2>&1
cp -r results $out
'';
passthru.variants = stage {
name = "strelka-call-variants";
buildCommand = ''
ln -s ${drv}/variants/variants.vcf.gz $out
'';
passthru.filetype = filetype.gz (filetype.vcf {ref=ref;});
};
}
|
