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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;
in
assert (length (unique refs) == 1);
let
out = stage {
name = "strelka-call";
buildInputs = with pkgs; [ strelka ];
outputs = [ "out" "variants" ];
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
# Strelka writes runtime stats and timestamps;
# both have to be stripped to provide determinism
cd results/variants
rm *.tbi genome.vcf.gz
for f in *.vcf.gz; do
gunzip $f
g=$(basename $f .gz)
sed -i '/^##fileDate/d' $g
sed -i '/^##startTime/d' $g
done
mv variants.vcf $variants
ln -s $variants variants.vcf
mkdir $out
cp -r * $out
'';
passthru.multicore = true;
};
ft = {filetype = types.filetype.vcf {ref = ref;};};
in out // { variants = out.variants // ft; }
|
