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Adding pretext ingestion docs #145

Merged
merged 25 commits into from
Sep 25, 2023
Merged

Adding pretext ingestion docs #145

merged 25 commits into from
Sep 25, 2023

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DLBPointon
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Adding just the pretext ingestion information

@DLBPointon DLBPointon added the Release 1 Issues required for first release label Sep 21, 2023
@DLBPointon DLBPointon self-assigned this Sep 21, 2023
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github-actions bot commented Sep 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3d5ea17

+| ✅ 126 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-09-25 10:30:39

priyanka-surana
priyanka-surana previously approved these changes Sep 21, 2023
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Please fix the highlighted typo. Otherwise good with me.

docs/usage.md Show resolved Hide resolved
@DLBPointon @priyanka-surana
Update docs/usage.md
c4620c9 
Co-authored-by: Priyanka Surana <[email protected]>
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Hi @priyanka-surana

We now have a hot fix incoming for the CUSTOM_GETCHROMSIZES which has mangled the genomeark assemblies. This will be alongside all the docs changes we've spoken about on Slack.

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We now have a hot fix incoming for the CUSTOM_GETCHROMSIZES which has mangled the genomeark assemblies. This will be alongside all the docs changes we've spoken about on Slack.

Can we do them in separate PRs please? This will speed up the review process as we can do them independently.

@priyanka-surana priyanka-surana dismissed their stale review September 21, 2023 15:21

New files added

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Removed hotfix from this PR

In separate PR

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DLBPointon commented Sep 22, 2023 •
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Hi @priyanka-surana,
This latest push, adds all the docs to one file as requested.

There's a lot of HTML in there to shrink the footprint of it so hopefully that doesn't screw up website rendering, but locally this looks fine.

Thanks

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Merged dev into branch, due to a number of differences

@muffato muffato mentioned this pull request Sep 25, 2023
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muffato commented Sep 25, 2023

I pushed my changes (reformatting) to the branch mm49_docs_reformat, see https://github.com/sanger-tol/treeval/blob/mm49_docs_reformat/docs/usage.md

If you're happy with the changes, just merge that branch into here.

@DLBPointon DLBPointon merged commit 6df2644 into dev Sep 25, 2023
@DLBPointon DLBPointon deleted the More-docs branch September 25, 2023 12:10
@muffato muffato added this to the Release 1 milestone Sep 25, 2023
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@muffato muffato muffato approved these changes

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