{ 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; }