diff options
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 63 |
1 files changed, 31 insertions, 32 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index f90e3a9..afbdf68 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -54,37 +54,36 @@ let plot = cnvkit.scatterPlot {} cnvs; }; - testNaming = linkDrv [ - (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") - (ln cnvkitResults.cnvs "cnvkit") - (ln cnvkitResults.plot "cnvkit.pdf") - (ln tnpairResult.octopusVars "octopus.vcf") - (ln tnpairResult.octopusSomatic "octopus-somatic.vcf") - (ln tnpairResult.variants "strelka") - (ln tnpairResult.glvariants "strelka-gl") - (ln tnpairResult.variants.indels "strelka.indels.vcf") - (ln tnpairResult.variants.snvs "strelka.snvs.vcf") - (ln tnpairResult.glvariants.variants "strelka.gl.vcf") - (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") - (ln (bwa.mem {inherit ref;} tnpair.normal.files) "alignments/bwa-mem.bam") - (ln (bwa.mem2 {inherit ref;} tnpair.normal.files) "alignments/bwa-mem2.bam") - (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam") - (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam") - (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") - (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2") - (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3") - (ln (samtools.merge {} tnpairResult.shards) "alignments/merged-shards.bam") - (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam") - (ln (samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)]) "alignments/merged-namesorted.bam") - (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram") - #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram") - (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat") - #(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat") - (ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1") - #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") - #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") - #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") - (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}") - ]; + alignments = { + "bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files; + "bwa-mem.bam" = bwa.mem {inherit ref;} tnpair.normal.files; + "bwa-mem2.bam" = bwa.mem2 {inherit ref;} tnpair.normal.files; + "minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files; + "snap-normal.bam" = snap.align {inherit ref; } tnpair.normal.files; + "${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour; + }; + + testNaming = linkOutputs { + 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 = tnpairResult.variants; + strelka-gl = tnpairResult.glvariants; + strelka-indels = tnpairResult.variants.indels; + "strelka.snvs.vcf" = tnpairResult.variants.snvs; + "strelka.gl.vcf" = tnpairResult.glvariants.variants; + 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; + inherit alignments; + }; in testNaming |