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 = aligner: rg: x:
    nameSort (aligner {
        inherit ref;
        RG = {
          ID = rg;
          SM = 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 bwa.align x.name x.files)))) {inherit normal tumour;};
    bowtie-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bowtie.align x.name x.files)))) {inherit normal tumour;};
    bwa2-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bwa.mem2 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);
    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;
    "subread.bam" = subread.align {inherit ref;} tnpair.normal.files;
    "last.maf" = lastal.align {inherit ref;} tnpair.normal.files.input1;
    "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.octopusVars;} (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]);
    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]);
    gridssSomatic = gridss.filterSomatic {normalName = "mysample2";} (gridss.call (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}-targeted.cram" =
      samtools.view {
        outfmt = types.toCram;
        targets = "abcd\t10\t100";
      }
      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"];
    };
    mosdepth-targeted = mosdepth.plot {} {
      inputs = mapAttrsToList (_: mosdepth.depth {targets = ["abc\t10\t100"];}) tnpairResult.alignments;
      names = ["seq1" "seq2"];
    };
    xenomapper = xenomapper.allocate {} {
      primary = nameSort tnpairResult.alignments.tumour;
      secondary = nameSort tnpairResult.alignments.tumour;
    };
    quip = with quip; unquip {} (quip {} tnpairResult.alignments.tumour);
    genmap = genmap.calcmap {} ref;
    inherit alignments;
  };
in
  testNaming