diff options
| author | Justin Bedo <cu@cua0.org> | 2018-12-05 10:48:05 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-10 16:26:37 +1100 |
| commit | 86b1b192501eecc8a4e566795327772c32b1633d (patch) | |
| tree | f06d78c11672b66e2655ab5f23cfe91a30fe5504 /test-tnpair.nix | |
| parent | 16951e6f99636a2c9d924d49c549a918e403f276 (diff) | |
bowtie: init
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 11 |
1 files changed, 7 insertions, 4 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index a6ea163..b01d61e 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -21,7 +21,9 @@ let fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs); fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs); - alignWithRG = rg: bwa.align { ref = fetchfa ./example/ref.fa; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; + ref = fetchfa ./example/ref.fa; + + alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort {}; flagstat = samtools.flagstat {}; check = fastqc.check {}; @@ -35,7 +37,7 @@ let }; normal = {name = "mysample2"; files = { input1 = fetchfq ./example/sample2-1.fq; - input2 = fetchfq ./example/sample2-1.fq; + input2 = fetchfq ./example/sample2-2.fq; }; }; }; @@ -53,8 +55,9 @@ let mkdir $out 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 ${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 |