Fixes for

[jscaber]

Fixed errors in pipeline mapping

1. os.symlink instead of P.clone
2. mergeBAMFiles was not being called by "full"
3. removed nreads.dir/nreads.dir doubling up of subdirectories

[sebastian-luna-valero]

@nickilott can you please have a look at this, taking into account our conversation in https://github.com/cgat-developers/cgat-flow/pull/21 and https://github.com/CGATOxford/CGATPipelines/pull/420

[sebastian-luna-valero]

I will have a look at why P.clone() does not work.

[sebastian-luna-valero]

So IMHO P.clone() should not be there in the first place. The goal of that if statement is to create a fake output file so ruffus is happy. I agree the symlink is an appropriate solution here.

[sebastian-luna-valero]

Let's wait for @nickilott's feedback about the nreads.dir/%s.nreads vs %s.nreads issue before merging.

[Acribbs]

Have these changes been through pipeline testing? I remember that we removed mergeBAMFiles from the full task for a pipeline testing reason, but I have forgotten the reason why now.

[nickilott]

Hi,

I will look at this tomorrow morning, apologies if this holds things up but I work Wednesday-Friday

Nick

---

Dr Nicholas Ilott

Kennedy Institute of Rheumatology

University of Oxford

nicholas.ilott@kennedy.ox.ac.uk

Note that I work at the KIR on Wednesdays, Thursdays and Fridays

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From: Sebastian Luna-Valero notifications@github.com Sent: Friday, July 20, 2018 2:47:38 PM To: cgat-developers/cgat-flow Cc: Nicholas Ilott; Mention Subject: Re: [cgat-developers/cgat-flow] Fixes for (#43)

Let's wait for @nickilotthttps://github.com/nickilott's feedback about the nreads.dir/%s.nreads vs %s.nreads issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/cgat-developers/cgat-flow/pull/43#issuecomment-406605664, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFOY-Ng7_8QJaIhjZnV0z5mt47kbkpUCks5uId96gaJpZM4VX5xy.

[sebastian-luna-valero]

That's alright. Thanks, Nick.