Enable organelles subworkflow

ksenia-krasheninnikova commented 9 months ago

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[bot] commented 9 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit d99f5cc

+| ✅ 130 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `conf/igenomes.config` * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Check the defaults for all processes_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Customise requirements for specific processes._ ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomeassembly_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomeassembly_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomeassembly_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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ksenia-krasheninnikova commented 9 months ago

@gq1 The purpose of this PR is to try setting the borrowed NCBI API key to check if it solves request errors on tower.

muffato commented 8 months ago

I've done some digging. The environment variable NCBI_API_KEY is only recognised by the Entrez CLI, not BioPython.

See this part of the stack-trace

    File "/opt/MitoHiFi/findMitoReference.py", line 39, in find_full_mito
      handle = Entrez.esearch(db="nucleotide",term=term, idtype="acc")

The documentation https://biopython.org/docs/1.75/api/Bio.Entrez.html#module-Bio.Entrez says there is an api_key parameter that needs to be set.

MitoHifi itself (specifically the findMitoReference.py script) needs to be changed to take the API key (from the command-line or the environment) and pass it to the Entrez module:

Either by adding api_key=... to every Entrez function call like the one above
Or by setting it once for all
```
Entrez.api_key = ...
```
at the beginning of the script

ksenia-krasheninnikova commented 8 months ago

@muffato thank you very much for looking into it I misread the docs and hoped setting the env variable will be enough. In this case I can update the findMitoReference.py script but this will require rebuilding of the docker/singularity image which might take time for back and forth with the MitoHiFi maintainer. I suggest I switch off organelles_on flag in github testing for now and we release the pipeline as is with the further updates on organelles subworkflow in release 1.1 that would also contain the oatk module so it all adds up nicely.

gq1 commented 6 months ago

@ksenia-krasheninnikova Why you increased the runner from 8c to 16c? The 8c runner failed not because the space, the error message is: curl: (6) Could not resolve host: darwin.cog.sanger.ac.uk

ksenia-krasheninnikova commented 6 months ago

@gq1 Yes, I assumed it's some server configuration related issue which made it unapplicable. But also, the host that we used to run it when we made the release was the 16c one. I don't recall all the details but it must be because the smaller ones were not enough.

gq1 commented 6 months ago

Here are the resources, can we give 4c or 8c a try again?

4 | 16 GB | 150 GB | Ubuntu 8 | 32 GB | 300 GB | Ubuntu, Windows 16 | 64 GB | 600 GB | Ubuntu, Windows

ksenia-krasheninnikova commented 6 months ago

Worked from the second attempt on 8c. It didn't work on 4c initially throwing not enough disk space error.

gq1 commented 6 months ago

I can't see 4c being used in the recent commit, 150G disk space, quite lots. Maybe we can give another try.

ksenia-krasheninnikova commented 6 months ago

Works fine with 4c. I thought ubuntu-latest is 4c herein the confusion.

ksenia-krasheninnikova commented 5 months ago

NCBI API key for ToL API is added to the repo by @muffato
A docker image for the new release of mitohifi supporting NCBI API key in findMitoReference.py script is being pulled.

Pipeline logic slightly changed:

organelles workflow is run over the raw contigs instead of purged;
purging-wise: haplotigs are not purged, instead haplotigs removed from the primary assembly are joined with hifiasm haplotigs

ksenia-krasheninnikova commented 5 months ago

Thank you @gq1 and @muffato ! Merging into dev.

sanger-tol / genomeassembly