nf-core
Add umicollapse as an alternative to umi-tools
TODO:
- [X] Benchmark paired ends mode
- [x] Include in multiqc - https://github.com/MultiQC/MultiQC/pull/2814
- [x] Decide if
PREPARE_FOR_SALMONis needed - [ ] Update umicollapse version.
- [ ] Update Changelog.
I checked the output of UMICollapse, and it definitely does not follow the assumptions stated in prepare_for_rsem.py. So PREPARE_FOR_RSEM will be needed for UMICollapse as long as it is needed for umi-tools.
@MatthiasZepper all remaining tasks are now done. Please take another look.
@MatthiasZepper all remaining tasks are now done. Please take another look.
Unfortunately, the UMICollapse module has not yet been upgraded...
@siddharthab: The module is finally upgraded, so you can replace the local path with the up-to-date module.
@siddharthab: The module is finally upgraded, so you can replace the local path with the up-to-date module.
Thanks. Can you check if everything looks good now? I just ran nf-core modules update umicollapse, but do not know if I need to do more.
Sorry, good in principle now for me (maybe some factoring out we can do later). Just need to get tests to run + pass.
Sorry, good in principle now for me (maybe some factoring out we can do later). Just need to get tests to run + pass.
Well, it appears the issue is on my end. Will fix asap! Sorry!
The UMICollapse tests are failing, because they try importing the BWA-Mem module, which isn’t included in this pipeline. As obviously everything is available in the modules directory, the tests pass in that context.
Considering that I had copied the tests from umitools dedup due to my limited experience with nf-test when creating the UMICollapse module, I was puzzled about why the umitools-tests work in here for the pipeline.
Turns out that I had coicidentially copied them as a template during a very brief period on March 4 before Maxime updated them again, which explains the discrepancy...
Long story short, I will have to fix the UMICollapse test in the modules directory to be self-reliant.
Just to give a brief update: I have finally found some time to update the tests. Therefore, I hope the module tests will soon be updated in the repo and subsequently this PR also be merged successfully!
@maxulysse: Let me know, when you have synced the test data to the S3 bucket. Ultimately, that sounds like something we could automate in the future with a CI on the test data repository?
Restore truncated CHANGELOG.md with 3.0 and prior releases.
:facepalm:
I did not see that missing when I fixed the merge conflicts, good catch @MatthiasZepper
@nf-core-bot fix linting
Thanks! Strange, that the linter is unhappy, since I literally copy and pasted that from the current dev...anyway.