aboutsummaryrefslogtreecommitdiff
path: root/test-tnpair.nix
diff options
context:
space:
mode:
Diffstat (limited to 'test-tnpair.nix')
-rw-r--r--test-tnpair.nix101
1 files changed, 53 insertions, 48 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 6eb2e23..9ba0e51 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,4 +1,4 @@
-with import <bionix> {};
+with import <bionix> { };
with lib;
let
@@ -6,28 +6,32 @@ let
name = baseNameOf path;
buildCommand = "ln -s ${path} $out";
};
- fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
- fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
+ fetchfq = attrs: types.tagFiletype (types.filetype.fq { }) (fetchlocal attrs);
+ fetchfa = attrs: types.tagFiletype (types.filetype.fa { }) (fetchlocal attrs);
ref = fetchfa ./examples/ref.fa;
- alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";} x);
- sort = samtools.sort {};
- nameSort = samtools.sort {nameSort = true;};
- flagstat = samtools.flagstat {};
- check-fastqc = fastqc.check {};
- check-fastp = fastp.check {};
- callVariants = strelka.callSomatic {};
- markdup = samtools.markdup {};
- fixmate = samtools.fixmate {};
+ alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${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 = {
+ tumour = {
+ name = "mysample1";
+ files = {
input1 = fetchfq ./examples/sample1-1.fq;
input2 = fetchfq ./examples/sample1-2.fq;
};
};
- normal = {name = "mysample2"; files = {
+ normal = {
+ name = "mysample2";
+ files = {
input1 = fetchfq ./examples/sample2-1.fq;
input2 = fetchfq ./examples/sample2-2.fq;
};
@@ -37,36 +41,36 @@ let
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);
+ 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;
- "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;
+ "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;
+ "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 ];};
+ 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;
@@ -74,24 +78,25 @@ 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]);
- 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]; tumour = tumour;});
- mantaT = manta.call {} (with tnpairResult.alignments; {tumour = 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)];
- "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour);
+ delly = delly.call { } (with tnpairResult.alignments; [ normal tumour ]);
+ lumpy = lumpy.call { } (with tnpairResult.alignments; [ normal tumour ]);
+ manta = manta.call { } (with tnpairResult.alignments; { normals = [ normal tumour ]; });
+ mantaTN = manta.call { } (with tnpairResult.alignments; { normals = [ normal ]; inherit tumour; });
+ mantaT = manta.call { } (with tnpairResult.alignments; { inherit tumour; });
+ gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]);
+ gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]);
+ gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]);
+ "merged-shards.bam" = samtools.merge { } tnpairResult.shards;
+ "merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ];
+ "merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ];
+ "${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; };
+ 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; };
inherit alignments;
};
-in testNaming
+in
+testNaming
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-07 06:09:23 +0000