with import <bionix> { };
with lib;

let
  fetchlocal = path: pkgs.stdenv.mkDerivation {
    name = baseNameOf path;
    buildCommand = "ln -s ${path} $out";
  };
  fetchfq = attrs: types.tagFiletype (types.filetype.fq { }) (fetchlocal attrs);
  fetchfa = attrs: types.tagFiletype (types.filetype.fa { }) (fetchlocal attrs);

  ref = fetchfa ./examples/ref.fa;

  alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'"; } x);
  sort = sambamba.sort { };
  nameSort = sambamba.sort { nameSort = true; };
  flagstat = samtools.flagstat { };
  check-fastqc = fastqc.check { };
  check-fastp = fastp.check { };
  callVariants = strelka.callSomatic { };
  markdup = samtools.markdup { };
  fixmate = samtools.fixmate { };

  tnpair = {
    tumour = {
      name = "mysample1";
      files = {
        input1 = fetchfq ./examples/sample1-1.fq;
        input2 = fetchfq ./examples/sample1-2.fq;
      };
    };
    normal = {
      name = "mysample2";
      files = {
        input1 = fetchfq ./examples/sample2-1.fq;
        input2 = fetchfq ./examples/sample2-2.fq;
      };
    };
  };

  processPair = { tumour, normal }: rec {
    alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
    variants = callVariants alignments;
    octopusSomatic = octopus.callSomatic { } { inherit (alignments) normal; tumours = [ alignments.tumour ]; };
    glvariants = strelka.call { } (builtins.attrValues alignments);
    platypusVars = platypus.call { } (builtins.attrValues alignments);
    octopusVars = octopus.call { } (builtins.attrValues alignments);
    shards = map (x: nameSort (bwa.align { inherit ref; } x)) (shard.fastQPair 2 normal.files);
  };

  tnpairResult = processPair tnpair;

  cnvkitResults = rec {
    cnvs = cnvkit.callCNV { } (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ]; });
    plot = cnvkit.scatterPlot { } cnvs.out1;
  };

  alignments = {
    "bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
    "last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
    "whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
    "bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
    "bwa-mem2.bam" = bwa.mem2 { inherit ref; } tnpair.normal.files;
    "minimap2-normal.bam" = minimap2.align { inherit ref; preset = "sr"; } tnpair.normal.files;
    "snap-normal.bam" = snap.align { inherit ref; } tnpair.normal.files;
    "${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour;
    "hisat2-normal.bam" = hisat2.align { inherit ref; } tnpair.normal.files;
  };

  testNaming = linkOutputs {
    crai = samtools.index { } (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour);
    kallisto = kallisto.quant { inherit ref; } (attrValues tnpair.tumour.files);
    facets = facets.callCNV { } { vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ]; };
    cnvkit = cnvkitResults.cnvs;
    "cnvkit.pdf" = cnvkitResults.plot;
    "octopus.vcf" = tnpairResult.octopusVars;
    "octopus-somatic.vcf" = tnpairResult.octopusSomatic;
    strelka-indels = tnpairResult.variants.indels;
    "strelka.snvs.vcf" = tnpairResult.variants.snvs;
    "strelka.gl.vcf" = tnpairResult.glvariants;
    delly = delly.call { } (with tnpairResult.alignments; [ normal tumour ]);
    lumpy = lumpy.call { } (with tnpairResult.alignments; [ normal tumour ]);
    manta = manta.call { } (with tnpairResult.alignments; { normals = [ normal tumour ]; });
    mantaTN = manta.call { } (with tnpairResult.alignments; { normals = [ normal ]; inherit tumour; });
    mantaT = manta.call { } (with tnpairResult.alignments; { inherit tumour; });
    gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]);
    gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]);
    gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]);
    "merged-shards.bam" = samtools.merge { } tnpairResult.shards;
    "merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ];
    "merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ];
    "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour;
    "${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1;
    "${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files;
    snver = snver.call { ploidy = 1; } tnpairResult.alignments;
    mosdepth = mosdepth.plot { } { inputs = mapAttrsToList (_: mosdepth.depth { }) tnpairResult.alignments; names = [ "seq1" "seq2" ]; };
    xenomapper = xenomapper.allocate { } { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
    genmap = genmap.calcmap { } ref;
    inherit alignments;
  };

in
testNaming