diff options
| author | l-d-s <l@sdf.org> | 2019-05-01 14:04:54 +1000 |
|---|---|---|
| committer | l-d-s <l@sdf.org> | 2019-05-01 14:05:00 +1000 |
| commit | 95c8a36a7e673fac090175729069a668daa919da (patch) | |
| tree | 7807cd59d5645864769d6e89b17ff43ed63c0d55 /test-tnpair.nix | |
| parent | d517a934f570427e46be8d83aa2ae4b045b069e8 (diff) | |
Add fastp.
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 12 |
1 files changed, 7 insertions, 5 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 1d281fa..1b5f347 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -14,7 +14,8 @@ let alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort {}; flagstat = samtools.flagstat {}; - check = fastqc.check {}; + check-fastqc = fastqc.check {}; + check-fastp = fastp.run {}; callVariants = strelka.callSomatic {}; markdup = samtools.markdup {}; fixmate = samtools.fixmate {}; @@ -59,10 +60,11 @@ let #(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/${tnpair.normal.name}.2") + (ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1") + #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") + #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") + #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") + (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}") ]; in testNaming |