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| author | Justin Bedo <cu@cua0.org> | 2018-10-29 15:33:53 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-29 15:36:33 +1100 |
| commit | e7cd661d1c5fb4135e3d436e151294e26aef9127 (patch) | |
| tree | 71ef7647d15d57bc2db2cf8ec532da794fddb2fa /test-tnpair.nix | |
| parent | 8fb986fd88705fc01be7145b04fa229092c1e69e (diff) | |
Split gridss into constituents
Wrap each individual command for GRIDSS so that bionix executed the pipeline
rather than GRIDSS. This patch introduces a "call" function that executed the
whole pipeline in bionix on an arbitrary BAM file.
Resolves #10.
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 1 |
1 files changed, 1 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 0f6a441..a6ea163 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -54,6 +54,7 @@ let ln -s ${tnpairResult.variants} $out/strelka mkdir $out/alignments ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss + ln -s ${gridss.call (with tnpairResult.alignments; [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 |