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-rw-r--r--test-tnpair.nix159
1 files changed, 99 insertions, 60 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 195ac27..ac8d0bb 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,25 +1,32 @@
-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);
+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 { };
+ 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 = {
@@ -38,42 +45,56 @@ let
};
};
- 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; };
+ 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);
- 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);
+ 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;
+ 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;
+ "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;
+ "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; } (with tnpairResult.alignments; [ normal tumour ]);
+ 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;} (with tnpairResult.alignments; [normal tumour]);
cnvkit = cnvkitResults.cnvs;
"cnvkit.pdf" = cnvkitResults.plot;
"octopus.vcf" = tnpairResult.octopusVars;
@@ -81,27 +102,45 @@ let
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) ];
- "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour;
+ delly = delly.call {} (with tnpairResult.alignments; [normal tumour]);
+ manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour];});
+ mantaTN = manta.call {} (with tnpairResult.alignments; {
+ normals = [normal];
+ inherit tumour;
+ });
+ mantaT = manta.call {} (with tnpairResult.alignments; {inherit tumour;});
+ gridss = gridss.callVariants {} (with tnpairResult.alignments; [normal tumour]);
+ gridss2 = gridss.call (with tnpairResult.alignments; [normal tumour]);
+ gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour]);
+ gridssSomatic = gridss.filterSomatic {normalName = "mysample2";} (gridss.call (with tnpairResult.alignments; [normal tumour]));
+ "merged-shards.bam" = samtools.merge {} tnpairResult.shards;
+ "merged.bam" = samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal];
+ "merged-namesorted.bam" = samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)];
+ "${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" ]; };
- xenomapper = xenomapper.allocate { } { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
+ 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;
+ genmap = genmap.calcmap {} ref;
inherit alignments;
};
-
in
-testNaming
+ testNaming
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-07 21:18:32 +0000