diff options
| author | Justin Bedo <cu@cua0.org> | 2019-04-07 21:10:00 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-04-07 21:10:00 +1000 |
| commit | e97bc0b22b9f49d95d6b449b2b20e7222b42622d (patch) | |
| tree | 36b05f35f29ec5bbabd981fd83a69964fa285174 /test-tnpair.nix | |
| parent | 761d47937eeb6787ff807c34be7a3623a4bde0e9 (diff) | |
Update example data and expand tests
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 13 |
1 files changed, 8 insertions, 5 deletions
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 |