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Add documentation for running without Internet access #389

Merged
merged 11 commits into from
Aug 17, 2023
Merged

Add documentation for running without Internet access #389

merged 11 commits into from
Aug 17, 2023

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fa2k
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@fa2k fa2k commented Jul 26, 2023

This change adds a section to usage.md to describe running offline, including how to get nf-validation working. #387

I have run nf-core lint and there aren't any issues with usage.md.

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
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @fa2k,

It looks like this pull-request is has been made against the fa2k/raredisease 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 fa2k/raredisease 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!

@fa2k fa2k changed the base branch from master to dev July 26, 2023 08:55
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github-actions bot commented Jul 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b201395

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-17 09:24:34

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fa2k commented Jul 26, 2023 •
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Sorry I forgot something. Hold on for the next commit please.

Edit: I've amended the first commit and pushed this.

asp8200
asp8200 reviewed Jul 26, 2023
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docs/usage.md Outdated
Here is an example command to download pipeline version 1.1.0 with singularity images:

```
nf-core download \
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When I run that command with the latest version of nf-core (v2.9), I get:

 No such option: --container (Possible options: --container-cache-index, --container-library,     │
│ --container-system)

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Sorry about that. Seems they have changed the CLI since I downloaded nf-core tools

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I would just refer to the general docs on the website

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Ok, makes sense. I will remove the example.

asp8200
asp8200 reviewed Jul 26, 2023
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docs/usage.md Outdated
id '[email protected]'
}
```
This should go in your Nexflow confgiguration file, specified with `-c <YOURCONFIG>` when running the pipeline.
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Suggested change
This should go in your Nexflow confgiguration file, specified with `-c <YOURCONFIG>` when running the pipeline.
This should go in your Nextflow configuration file, specified with `-c <YOURCONFIG>` when running the pipeline.

asp8200
asp8200 reviewed Jul 26, 2023
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docs/usage.md Outdated
```
For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters).

Contrary to the paragraph about Nextflow on the nf-core tools page, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly:
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@asp8200 asp8200 Jul 26, 2023 •
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Not sure which homepage and packages you are referring to there. Perhaps you mean https://nf-co.re/tools ?

I didn't find any "paragraph about Nextflow" on https://nf-co.re/tools

EDIT: Perhaps you're referring to https://nf-co.re/docs/usage/offline#nextflow ?

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I've added another link, hope it makes sense like that

@fa2k @ramprasadn
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Co-authored-by: Ramprasad Neethiraj <[email protected]>
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fa2k commented Jul 26, 2023

Sorry about all these problems, and thanks for the suggestions.

ramprasadn
ramprasadn approved these changes Jul 26, 2023
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Nice work, @fa2k! Thanks for adding this!

LGTM! 🚀

@ramprasadn ramprasadn linked an issue Jul 26, 2023 that may be closed by this pull request
nf-validation makes it difficult to run without Internet access #387
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@ramprasadn ramprasadn merged commit cf78b22 into nf-core:dev Aug 17, 2023
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@ramprasadn ramprasadn ramprasadn approved these changes

@asp8200 asp8200 asp8200 approved these changes

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nf-validation makes it difficult to run without Internet access
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