From e97bc0b22b9f49d95d6b449b2b20e7222b42622d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Sun, 7 Apr 2019 21:10:00 +1000 Subject: Update example data and expand tests --- test-tnpair.nix | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) (limited to 'test-tnpair.nix') diff --git a/test-tnpair.nix b/test-tnpair.nix index 8b268ec..da37068 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -45,18 +45,21 @@ let (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln tnpairResult.variants "strelka") (ln tnpairResult.glvariants "strelka-gl") + (ln (strelka.indels tnpairResult.variants) "strelka.indels.vcf") + (ln (strelka.snvs tnpairResult.variants) "strelka.snvs.vcf") + (ln (strelka.variants tnpairResult.glvariants) "strelka.gl.vcf") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2") (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.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 (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/${tnpair.normal.name}.flagstat") + #(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat") (ln (check tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1") - (ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") - (ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") - (ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") + #(ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") + #(ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") + #(ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") ]; in testNaming -- cgit v1.2.3