diff options
| author | Justin Bedo <cu@cua0.org> | 2018-12-19 09:55:29 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-19 09:55:29 +1100 |
| commit | 0808fc803e3226d2f478229832bb827d7dfcbd0d (patch) | |
| tree | 6048e23151a9c0e183e59b964fd9ec5fa32df823 /test-tnpair.nix | |
| parent | 8501b505c9cec5768b2f1dfcb49f13e0f0611011 (diff) | |
link: introduce high-level linking functions
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 36 |
1 files changed, 15 insertions, 21 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index b01d61e..b897366 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -49,26 +49,20 @@ let tnpairResult = processPair tnpair; - testNaming = stdenv.mkDerivation { - name = "test-naming"; - buildCommand = '' - mkdir $out - ln -s ${tnpairResult.variants} $out/strelka - mkdir $out/alignments - ln -s ${bowtie.align {inherit ref;} tnpair.normal.files} $out/alignments/bowtie-normal.bam - ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])} $out/gridss - ln -s ${gridss.call (with tnpairResult.alignments; [normal tumour])} $out/gridss2 - ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam - ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram - ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram - ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat - ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat - mkdir $out/fastqc - ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1 - ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2 - ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1 - ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2 - ''; - }; + testNaming = linkDrv [ + (ln tnpairResult.variants "strelka") + (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 (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat") + (ln (flagstat tnpairResult.alignments.normal) "alignments/${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") + ]; in testNaming |