Adapt code and docs to nf-core template

[lpantano]

This PR adapt the code and docs to the latest nf-core template.

It is a mixed approach between manual copy/paste and git merge. I will need somebody to look into the most important thing I cannot miss since I am not sure if I covered all.

Thanks!

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md

[drpatelh]

This looks great @lpantano ! I've spotted a couple of things that may need to be changed but I'm looking on my mobile which isn't the greatest...Can have a look next week or before if I get some time.

You should be able to correct the markdownlint errors in the docs:
https://github.com/DavidAnson/markdownlint

Should the pipeline running end-to-end with the test dataset? If not, it would be great if you could do that before we merge this PR.

It looks like the test dataset failed because the gtf file couldn't be found. It does exist though so Travis may need to be restarted. I've been seeing that quite a bit over the last couple of days.

[lpantano]

Thanks for the quick look! yes, lets do it next week, not in a rush. It passed the test using docker in my computer, I’ll check again anyway. oh shuu, I forgot about the markdown lint, I’ll fix that as well, thanks for the pointer!

…

On May 24, 2019 at 18:43:55, Harshil Patel ***@***.***) wrote: This looks great @lpantano <https://github.com/lpantano> ! I've spotted a couple of things that may need to be changed but I'm looking on my mobile which isn't the greatest...Can have a look next week or before if I get some time. You should be able to correct the markdownlint errors in the docs: https://github.com/DavidAnson/markdownlint Should the pipeline running end-to-end with the test dataset? If not, it would be great if you could do that before we merge this PR. It looks like the test dataset failed because the gtf file couldn't be found. It does exist though so Travis may need to be restarted. I've been seeing that quite a bit over the last couple of days. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=AAML6HHJM4QY2IBWO2Q4PCTPXBVSXA5CNFSM4HPS7IV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWGWTLQ#issuecomment-495806894>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAML6HCXMY6UVGW7FUQW3ILPXBVSXANCNFSM4HPS7IVQ> .

[drpatelh]

Mainly minor issues @lpatano! Looking good. I still have to have a look at main.nf properly but Ive had a look at the rest of the files.

[apeltzer]

Some smallish things , otherwise 100% in line with @drpatelh 's comments - go Lorena :-) 👍

[lpantano]

Thanks so much for looking into this @drpatelh, @apeltzer. I will work on this in the next two days and trying not to miss any of the changes you propose.

[drpatelh]

Finished going through main.nf 👍

[lpantano]

ok, I think I fixed all the comments, but maybe I misunderstood any, if you could check it would be great. I have two main questions:

• versions of R packages should be included as well in the software version chunk?
• the multiqc_config.yaml file is correct?

Thanks!

[drpatelh]

@lpantano Looking much better! Mostly formatting issues that hopefully shouldnt take too long to resolve 👍

[lpantano]

ok, I think I added all the changes. Let me know if you spot something off. As well, not sure what I have to do with the TEMPLATE branch. I am making all my changes in the merge versions, so...can be the TEMPLATE the same than dev as a first version when this is in good shape?

[drpatelh]

Almost there @lpantano 😄

Thank you!

[drpatelh]

Great work @lpantano . We finally got there 😃 The template and overall structure looks good to me. I havent looked at the processes much but I guess you are going to develop that more now anyway.

Review points have been addressed

[lpantano]

wooo happy weekend! yes, I will develop from here!