Get raw gene count tables from either Salmon and RSEM analysis

[qbicStefanC]

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• This comment contains a description of changes (with reason).
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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 :)