Get raw gene count tables from either Salmon and RSEM analysis

[qbicStefanC]

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!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @qbicStefanC,

It looks like this pull-request is has been made against the qbicStefanC/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the qbicStefanC/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[qbicStefanC]

Hi @WackerO
I created this to get (back) the raw counts from the Salmon/RSEM paths inside rnadeseq. I think the changes in the file are abvious. I have tested it with a real project dataset (QTRRI) and with the test profile and made sure other files or results are unchanged. I think that part is fine . What I am still a bit unsure about is the extraction of the raw counts either how i did it with : assay(cds) or alternatively with counts(cds). In above mentioned project it did not make a difference but maybe once could test this again. Thanks,S

[WackerO]

Hello @qbicStefanC, thanks for the PR! I think the assay() function is fine.

It would be nice if you could update the test YMLs (https://github.com/qbic-pipelines/rnadeseq/blob/master/tests/test_star_salmon.yml and https://github.com/qbic-pipelines/rnadeseq/blob/master/tests/test_star_rsem.yml) by adding entries for the new matrices that are output; you just need to run those two tests (i.e. nextflow run main.nf -profile cfc,test_star_rsem and test_star_salmon) and generate the md5sums for the matrices.

Also, please update the https://github.com/qbic-pipelines/rnadeseq/blob/dev/CHANGELOG.md by copy-pasting an older entry to the top and modifying the line :)

[qbicStefanC]

Hi @WackerO ,
I think I have done as requested and updated the test YMLs (see here qbicStefanC@4fc1d15 and here qbicStefanC@9e1c23e ) by adding entries for the raw gene count matrices.

I also minimalistically updated the changelog (https://github.com/qbic-pipelines/rnadeseq/blob/dev/CHANGELOG.md by copy-pasting an older entry to the top and modifying the line :). Please check and let me know.S

[WackerO]

Hey @qbicStefanC, thanks for the tests! The changelog looks good, can you resolve the conflict so we can see if the new tests succeed?

[qbicStefanC]

resolved the conflict on the changelog...

[WackerO]

Thanks for the work, Stefan! I just removed some trailing whitespaces so prettier won't complain. The tests should now all run (except for linting), so after that is done, I'll override the protection and merge :)

[WackerO]

The remaining tests fail due to an old template, will override and merge