have updated regex of ruffus command for mergeReadCounts because it w…

[Acribbs]

…as incorrectly written

[sebastian-luna-valero]

Hi,

This reverts the changes in #21 .

Could @Acribbs and @nickilott please have a look and decide what's the best way forward?

Best regards,
Sebastian

[Acribbs]

mergeBAMFiles (and hence mergeReadCounts) is no longer in the full task because it breaks the pipeline testing (if I remember rightly), therefore this function is not tested at the moment. So if the mergeReadCounts is activated it results in a nreads.dir/nreads.dir/{sample_name}.nreads, it should be nreads.dir/{sample_name}.nreads. The pipeline won't run mergeBAMFiles because the regular expression is wrong.

I have ran mapping using the committed code and it works now.

[sebastian-luna-valero]

Thanks. For our reference, this was also removed by @jscaber in #43

@nickilott please let us know your thoughts.

[Acribbs]

Ah yes, this is exactly the issue I am correcting for here, may be better to merge @jscaber 's pull request then.

[nickilott]

Hi,
Yes the nreads.dir/nreads.dir should be changed as in #43 and above. The issue that I was having a problem with was loading the read counts (duplication) but this (as far as I can tell) is not changed in #43. I think it is fine to merge @jscaber pull request if everyone else is in agreement.

Apologies again for not responding sooner to this

Nick

[Acribbs]

I also agree

[sebastian-luna-valero]

Thanks, both.

Closing this in favor of #43