Release 2.0 fixes

[BethYates]

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]]

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[github-actions[bot]]

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

Posted for pipeline commit efc6169

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.2.2'`` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - 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[muffato]

I got this error in UPLOAD_HIGLASS_DATA when running the full test:

Command error:
  W1009 12:03:04.412509      41 loader.go:222] Config not found: /nfs/users/nfs_m/mm49/.kube/config.tol-it-dev-k8s
  W1009 12:03:04.450610      96 loader.go:222] Config not found: /nfs/users/nfs_m/mm49/.kube/config.tol-it-dev-k8s
  error: no current context is set

I can see the script does

export KUBECONFIG=~/.kube/config.tol-it-dev-k8s

and the file exists. I guess it doesn't work because the file is not given as an input file to the module so Nextflow cannot stage it properly, and the way I run the pipeline /nfs is not mounted automatically either.

Running the full test with --upload_higlass_data false works.

Given this is not needed for BGA, let's push that to the 2.0.1 release ?

[BethYates]

Also found a minor issue in the resulting note that can be addressed in 2.0.1. The collector name should be capitalised in

The specimen was collected by DOUGLAS BOYES (University of Oxford) and identified by DOUGLAS BOYES (University

I think this issue has been fixed by the latest changes I made to the populate_genome_notes_template.py script - the changes were necessary to fix a KeyError bug I found when running the pipeline on my wider test species

[BethYates]

Good for me !

By the way, minor thing, on the full test, It still says "University Of Oxford" even though you've got code to turn Of to of. Do you know why it's still happening ?

Douglas Boyes, $INTRO_WRITER, University Of Oxford Genome Acquisition Lab, University Of Oxford Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium

I'm not sure, I noticed this yesterday too but didn't have time to investigate. There's probably lots of other template changes we could make to how we handle authors and their affiliations as well as collector/identifier information in the methods section so we could address this when we look at that. This is something I've been talking to Karen about and I want to get the logic right with her before doing anything more.