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ENH: Allow pathogen-repo-ci to invoke workflow in subfolder #63

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corneliusroemer opened this issue Sep 25, 2023 · 2 comments
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ENH: Allow pathogen-repo-ci to invoke workflow in subfolder #63

corneliusroemer opened this issue Sep 25, 2023 · 2 comments
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enhancement New feature or request

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@corneliusroemer
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corneliusroemer commented Sep 25, 2023 •
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Context

Current pathogen-repo-ci seems to assume that we don't need to customize workdir in nextstrain build ., i.e. we can't set nextstrain build foobar.

Our nextstrain/pathogen-repo-template, however, puts the main workflow in a folder. So we should add that feature.

See https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1695664810319929 for discussion

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A clear and concise description of what you want to happen

Possible solution

Tried in #57 but introduce a bug in upload-artifact.
Tried to address in #62 but couldn't get it to work.

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@corneliusroemer corneliusroemer added the enhancement New feature or request label Sep 25, 2023
corneliusroemer added a commit to nextstrain/augur that referenced this issue Sep 26, 2023
@corneliusroemer
Disable monkeypox CI until pathogen-repo-ci supports custom build dir…
d5e5dc3 
…ectories

See issue nextstrain/.github#63
@corneliusroemer corneliusroemer mentioned this issue Sep 26, 2023
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corneliusroemer added a commit to nextstrain/augur that referenced this issue Sep 27, 2023
@corneliusroemer
Disable monkeypox CI until pathogen-repo-ci supports custom build dir…
5aba7ec 
…ectories (#1324)

See issue nextstrain/.github#63
@victorlin victorlin linked a pull request Oct 9, 2023 that will close this issue
Allow pathogen-repo-ci to run workflow in subdir via build-dir arg #62
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@victorlin victorlin mentioned this issue Oct 9, 2023
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@victorlin victorlin mentioned this issue Nov 2, 2023
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@victorlin
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zika no longer has a top-level workflow, increasing the need for this. I'll make PRs to disable it from all CI for now.

This was referenced Jan 19, 2024
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@joverlee521 joverlee521 mentioned this issue May 15, 2024
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genehack added a commit that referenced this issue May 22, 2024
@genehack
Update pathogen-repo-ci to better support CI [#63]
e1c3f55 
This adds the following features to the `pathogen-repo-ci` workflow:

* defines a `build-target` argument that will get passed to
  `nextstrain build` as a target directory — this allows the targeting
  of sub-dir based workflows, which was the main original issue in #63
* defines arguments (`download-previous-artifact`,
  `previous-artifact-name`) and a conditional step (`Dowload previous
  step artifact`) to support the downloading of the build artifact from
  a previous step to allow testing of later steps in a complete
  pathogen repo build

This combination of features was all that was needed to support [a CI
workflow for
`seasonal-cov`](nextstrain/seasonal-cov#11)
that:

1. runs an ingest workflow for a subset of the regular build data
2. uploads an artifact with the ingest output
3. downloads that artifact into a phylogenetic workflow
4. runs the phylogenetic workflow for the same subset of data
@genehack genehack mentioned this issue May 22, 2024
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@genehack genehack mentioned this issue May 31, 2024
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@joverlee521
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This has been superceded by #90

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Allow pathogen-repo-ci to run workflow in subdir via build-dir arg nextstrain/.github
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@victorlin @corneliusroemer @joverlee521