Major overhaul of docs #219

drpatelh · 2018-11-28T16:31:27Z

This comment contains a description of changes (with reason)
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated
CHANGELOG.md is updated
README.md is updated

Removed docs for profiles standard and none and changed description where applicable
Fixed a couple of broken links
Added new parameters --igenomesIgnore and --custom_config_version to usage.md
Rearranged sections in README.md and docs/README.md to be consistent
Added TODO statement in troubleshooting.md
Added some description for providing custom config profiles
Addressed a few other issues I noticed whilst writing nf-core/atacseq

codecov-io · 2018-11-28T16:37:14Z

Codecov Report

Merging #219 into dev will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev     #219   +/-   ##
=======================================
  Coverage   90.76%   90.76%           
=======================================
  Files           8        8           
  Lines         931      931           
=======================================
  Hits          845      845           
  Misses         86       86

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nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/configuration/adding_your_own.md

sven1103

Thanks a lot @drpatelh for this! Only minor things from my side to correct.

sven1103 · 2018-11-28T18:36:24Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md

@@ -242,7 +241,7 @@ Use to set a top-limit for the default CPU requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_cpus 1`

 ### `--plaintext_email`
-Set to receive plain-text e-mails instead of HTML formatted.
+Set to receive plain-text e-mails instead of HTML formatted.  


Added whitespace? I think this can be reverted

Should be fixed now in latest commit.

sven1103 · 2018-11-28T18:36:56Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md


-### `--multiqc_config`
+### `--multiqc_config`


Don't see a change here, probably different encoding?

Im a bit puzzled too.

The --multiqc_config section isnt rendered properly in the current usage.md:
https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/usage.md#--plaintext_email

Im not sure whether the whitespace in the comment above sorts it out but its correctly rendered in this version:
https://github.com/drpatelh/tools/blob/dev/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/usage.md#--multiqc_config

I got this working for the docs in nf-core/atacseq so I copied it across and looked at the diff. Weird but it seems to work. I was staring at it for ages!

It's a non breaking space that can be achieved by holding shift and pressing space*. It looks identical in text editors and GitHub, but breaks GitHub markdown processing. Delete and press space again carefully and everything will work as expected.

* Learnt from a frustratingly large number of times where I've done this myself

holy, @ewels wtf. Yeah next guess would have been to check character encoding ...

Seeing as what i have done is doing the trick is it ok to leave it as it is? Not sure if it's likely to break something else.

Should be fixed now in latest commit. I think...

…onfiguration/adding_your_own.md Co-Authored-By: drpatelh <drpatelh@users.noreply.github.com>

ewels · 2018-11-29T08:10:18Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md

-Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files in [`conf`](../conf) for examples.
+Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
+
+If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can request your custom config file to be added in the `pipelines` chat on the Slack messenger for `nf-core` (may need to be invited first!) or on the `nf-core/Lobby` group on Gitter.


No need to mention Gitter. Perhaps instead say that people can create a pull request with their config and should join slack to become a member of nf-core and ask for help..

Yes, we can drop gitter as we will most likely move everyone over to slack anyways...

Don't you have to be invited to join the Slack group? Or is that likely to change?

I was anticipating the rather tedious scenario where you ask for an invite via Gitter to join Slack...

No not anymore: https://nf-core-invite.herokuapp.com/

I also put this up to the Gitter channel (as top most message in the channel description) and we should add it to the main homepage...

Might add it to the homepage today with a logo, I guess its time

nf-core/website#56

Added details in latest commit.

ewels · 2018-11-29T08:10:45Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md

@@ -229,9 +225,12 @@ Specify the path to a specific config file (this is a core NextFlow command).

 Note - you can use this to override pipeline defaults.

+### `--custom_config_version`
+Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.


Maybe give an example of providing an exact commit ID..

Added in latest commit.

apeltzer

Looking good now :-)

apeltzer · 2018-11-29T12:06:37Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md

@@ -228,6 +230,11 @@ Note - you can use this to override pipeline defaults.
 ### `--custom_config_version`
 Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.

+```bash
+## Download and use config file with following git commid id
+--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96


sven1103 · 2018-11-29T16:28:04Z

thanks a lot @drpatelh for this contribution 🎉

drpatelh · 2018-11-29T16:37:09Z

@sven1103 Youre very welcome!

drpatelh added 8 commits November 28, 2018 16:13

Changed listing and added link to local installation

7293ada

Added bullet for reference genomes in line with docs README.md

fd5a1cc

Major overhaul, removal and addition of parameters

10013f2

Added a bit of info for providing custom config files

5fd3cf0

Bug-fixes and adding links to missing sections

34fdb74

Added TODO statment if parameters arent relevant

f5270e3

Fixed typo

11b776a

Added description of changes

199ac83

drpatelh mentioned this pull request Nov 28, 2018

Moved custom Institutional configs to nf-core configs on github #212

Merged

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sven1103 reviewed Nov 28, 2018

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sven1103 and others added 2 commits November 28, 2018 19:00

Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/c…

c74fc2d

…onfiguration/adding_your_own.md Co-Authored-By: drpatelh <drpatelh@users.noreply.github.com>

Removed whitespace

b94d148

ewels reviewed Nov 29, 2018

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drpatelh added 3 commits November 29, 2018 09:36

Merge branch 'dev' of https://github.com/drpatelh/tools into dev

cdef837

Minor change in description for custom configs

4d687f5

More details for custom config and example for --custom_config_version

4857789

apeltzer approved these changes Nov 29, 2018

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sven1103 approved these changes Nov 29, 2018

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sven1103 merged commit 3390899 into nf-core:dev Nov 29, 2018

drpatelh mentioned this pull request Dec 10, 2018

Put input files into channels nf-core/atacseq#4

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Major overhaul of docs #219

Major overhaul of docs #219

drpatelh commented Nov 28, 2018 •

edited by ewels

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Major overhaul of docs #219

Major overhaul of docs #219

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drpatelh commented Nov 28, 2018 •

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