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@ewels ewels commented Mar 13, 2019

I've been syncing nf-core/rnaseq with the template pipeline and found a few things in the template that needed tidying up and/or porting from the rnaseq.

Whilst I was there, I also added a new function to check the hostname against those set in nf-core/configs (see nf-core/configs#33) and throws a warning if it looks like the correct profile was not set.

Other stuff:

  • MultiQC report now added to the summary email in the template
  • nf-core/config params set to null to avoid warnings if not set
  • Automatically generated table of contents in markdown files (if used with Atom plugin)
  • Other general tidying

@drpatelh
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All looks good to me.

Are you going to make any more changes @ewels ?

Just waiting for Travis CI to pass.

@ewels
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ewels commented Mar 13, 2019

I'm not planning to make any changes for now, now. At least, not until I do the same process for other pipelines, but that'll be a different day / week / month.

Phil

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The last commit to CHANGELOG.md is not going to affect the tests because they passed beforehand. Going to merge before Travis CI completes.

@drpatelh drpatelh merged commit 9f2fe5d into nf-core:dev Mar 13, 2019
@ewels ewels mentioned this pull request Mar 13, 2019
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2 participants