Run qc on samples #102
Run qc on samples #102
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Also rename some confusing functions
| let fastqc_pipeline ~normal_samples ~tumor_samples ?rna_samples () = | ||
| let normal_fastqcs = | ||
| List.mapi | ||
| ~f:(fun i fq -> qc fq |> Bfx.save (sprintf "QC:normal-%d" i)) |
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Just a question, the FASTQ samples, don't they have different names that we could use there?
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Filed hammerlab/biokepi#387
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Agreed this would be superior, also filing in Epidisco #104
| ?rna_results ~parameters ~normal_bam_flagstat ~tumor_bam_flagstat ~fastqcs | ||
| = | ||
| let rna_bam_flagstat = | ||
| rna_results >>= fun {rna_bam_flagstat; _} -> return rna_bam_flagstat in |
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The open Option is too far up, Optionis not meant to be opened globally (Esp. since this case is actually anOption.maprather thanbind`).
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Seems reasonable.
Why is this an Option.map instead of/just as much a bind?
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Option.map shows that None stays None, and Some _ stays Some _ → less mental burden for the reader (?).
bind is more powerful in a way, so overkill here.
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@smondet back to you for a final look (I'm also reading over again to make sure this is sane) |
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@ihodes LGTM! |
fixes #101