docs: add extensive externally hosted docs #177
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fgypas
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.github/workflows/ci.yml
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| @@ -214,3 +216,35 @@ jobs: | |||
| - name: Run SRA downloads workflow | |||
| run: bash tests/test_sra_download_with_conda/test.local.sh | |||
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| integration-docker: | |||
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Test that pulls a zarp docker image and runs a test
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Cool to add a Dockerfile, test and docs for that, but I think that should go in a separate PR, if you don't mind.
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OK, moving it to another PR.
| ## Running ZARP without ZARP-cli | ||
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| 1. Assuming that your current directory is the workflow repository's root directory, |
| @@ -6,3 +6,4 @@ dependencies: | |||
| - python>=3.10, <3.12 | |||
| - snakemake<8 | |||
| - graphviz | |||
| - pyopenssl>=23.2.0 | |||
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The tests were failing with conda/conda#13619
I had to install pyopenssl
| @@ -65,4 +65,6 @@ extra: | |||
| nav: | |||
| - Home: README.md | |||
| - Installation: guides/installation.md | |||
| # ADD ADDITIONAL PAGES HERE | |||
| - Usage: guides/usage.md | |||
| @@ -1,5 +1,6 @@ | |||
| --- | |||
| channels: | |||
| - conda-forge | |||
uniqueg
changed the title
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Thanks a lot @fgypas and @mkatsanto 🙏
Looks pretty good, but there are still some issues. My comments mostly focused on the most prominent issues - there are still a bunch of issues I didn't check/comment on (and some areas I didn't even read thoroughly).
It would perhaps be good to run a spell checker and/or run it through GenAI to improve the wording and consistency in some parts. And definitely use a markdown linter.
Would also be good to ask @ninsch3000 for an additional review in the next round.
Finally, given that we change dependencies (environment.yml, samtools.yaml), I think we will need to create another release after we merge this, then update Zenodo and the manuscript and so on.
.github/workflows/ci.yml
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| @@ -214,3 +216,35 @@ jobs: | |||
| - name: Run SRA downloads workflow | |||
| run: bash tests/test_sra_download_with_conda/test.local.sh | |||
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| integration-docker: | |||
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Cool to add a Dockerfile, test and docs for that, but I think that should go in a separate PR, if you don't mind.
README.md
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| ```sh | ||
| zarp SRR23590181 | ||
| ``` |
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I guess the previous statement doesn't make sense if you remove this...
README.md
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| After successful execution - if all parameters could be either inferred or were specified by the user - `[OUTDIR]/[SAMPLES_OUT]` should contain a populated table with parameters `seqmode`, `f1_3p`, `f2_3p`, `organism`, `libtype` and `index_size` for all input samples as described in the [pipeline documentation][sample-doc]. | ||
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| You can also trigger ZARP without ZARP-cli. This is convenient for users who have some experience with snakemake and don't want to use a CLI to trigger their runs. Please head over to the [ZARP](https://zavolanlab.github.io/zarp/) documentation to learn how to start ZARP. |
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I think having to scroll down 193 lines to find a link to the ZARP docs is a bit strange. At this point readers might be convinced they have actually been reading the ZARP docs.
I would drastically shorten this document (just leave the absolute highlights)section and put a link to the docs in a much more prominent position.
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I made it similar to zarp-cli
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I updated the documentation based on the feedback. Can you please have a look again @uniqueg @ninsch3000? Thank you in advance. |
Description
Fixes #165
Type of change
Please delete options that are not relevant.
Conventional Commits guidelines
https://www.conventionalcommits.org/en/v1.0.0/
Changes to workflow inputs (sample table and/or configs)
Changes to workflow outputs
Everything else: patch
(add any other conventional commit in the beginning of the PR title)
Checklist: