Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Modernize repo #2

Open
30 tasks done
genehack opened this issue May 23, 2024 · 0 comments · May be fixed by #20
Open
30 tasks done

Modernize repo #2

genehack opened this issue May 23, 2024 · 0 comments · May be fixed by #20
Assignees
@genehack
Labels
enhancement New feature or request

Comments

@genehack
Copy link
Contributor

genehack commented May 23, 2024 •
edited
Loading

Rough plan of attack:
@genehack genehack added enhancement New feature or request source: office hours Issue mentioned during office hours labels May 23, 2024
@genehack genehack self-assigned this May 23, 2024
@genehack genehack removed the source: office hours Issue mentioned during office hours label May 23, 2024
genehack added a commit that referenced this issue May 23, 2024
@genehack
Archive previous contents under _LEGACY [#2]
f139941 
Once the repo modernization is complete, these files will be deleted;
for the moment this allows them to be easily accessed.
genehack added a commit that referenced this issue May 23, 2024
@genehack
Strip out old README; scaffold new one [#2]
2a8574c
genehack added a commit that referenced this issue May 23, 2024
@genehack
Add pre-commit-config.yaml and supporting files [#2]
df1a6dd 
Exclude the _LEGACY tree because there's no point in cleaning that
stuff up; leave a comment so I remember to go back and remove it when
`_LEGACY` goes away.
genehack added a commit that referenced this issue May 23, 2024
@genehack
Pull ingest and phylogenetic workflows from guide repo [#2]
3a2acd2 
Also apply pre-commit cleanup
@genehack genehack mentioned this issue May 23, 2024
Merged
genehack added a commit that referenced this issue May 24, 2024
@genehack
Update snakefmt pre-commit action [#2]
c25d878
genehack added a commit that referenced this issue May 29, 2024
@genehack
Sync with "standard" pre-commit-config [#2]
d823917 
Remove unused configuration files
This was referenced May 30, 2024
Merged
Closed
genehack added a commit that referenced this issue Jun 27, 2024
@genehack
Update .gitignore to match seasonal-cov [#2]
cdbd7f6
genehack added a commit that referenced this issue Jun 27, 2024
@genehack
Update ingest and make it work [#2]
f0e18fe 
* sync `ingest/README` with `seasonal-cov` version
* move from `defaults` to `config` for config files
* strip fetch-from-entrez stuff from config and rules files
* add `ncbi_taxon_id` to config
* strip guidance comments, light reformat of Snakemake and rules files
  for readability
* add benchmarks where missing
* remove unused nextclade bits
genehack added a commit that referenced this issue Jul 11, 2024
@genehack
Update ingest and make it work [#2]
f6795e7 
* sync `ingest/README` with `seasonal-cov` version
* move from `defaults` to `config` for config files
* strip fetch-from-entrez stuff from config and rules files
* add `ncbi_taxon_id` to config
* strip guidance comments, light reformat of Snakemake and rules files
  for readability
* add benchmarks where missing
* remove unused nextclade bits
* add "clean" convenience rule
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Phylogenetic workflow modernization [#2]
e6a0b1b 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Remove _LEGACY [#2]
093674c 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Misc cleanups and formatting [#2]
19a9f43 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Add .snakemake to clean rules [#2]
44d66ae
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Note why we're wildcarding a single thing [#2]
6578df9
@genehack genehack mentioned this issue Jul 18, 2024
Merged
1 task
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Phylogenetic workflow modernization [#2]
e6f2a81 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Remove _LEGACY [#2]
e535265 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Misc cleanups and formatting [#2]
044dd08 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Add .snakemake to clean rules [#2]
c473611
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Note why we're wildcarding a single thing [#2]
31c1ab7
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Phylogenetic workflow modernization [#2]
2b98ab2 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Remove _LEGACY [#2]
a9e739b 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Misc cleanups and formatting [#2]
be791e3 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Aug 2, 2024
@genehack
Add nextclade workflow [#2]
0431a05
genehack added a commit that referenced this issue Aug 2, 2024
@genehack
Add nextclade workflow [#2]
d57d611
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Add nextclade workflow [#2]
165eac6
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Merge pull request #10 from nextstrain/add-nextclade-build-2
1c8192b 
Add `nextclade` workflow [#2]
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
4f85ae3
@genehack genehack mentioned this issue Aug 5, 2024
Merged
1 task
genehack added a commit that referenced this issue Aug 22, 2024
@genehack
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
c9061d4
genehack added a commit that referenced this issue Aug 26, 2024
@genehack
Merge pull request #11 from nextstrain/use-nextclade-for-genotypes-2
525cb86 
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Download Nextclade dataset during ingest... [#2]
272d4c6 
...instead of depending on having one built locally.

Also corrects nextclade dataset name in the config.
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Add / tweak bits to allow upload of ingested files to S3 [#2]
5f61500
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Convert nextclade workflow to download inputs from S3 [#2]
12865fc
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Convert phylogenetic workflow to download inputs from S3 [#2]
52f3da5
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
We have a gene-specific build so we don't need this comment [#2]
55daabf
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Set explicit clock rate of 2e-04 ± 1e-05 [#2]
967c4e7
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Only run timetree on genome build [#2]
8f9dc75
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Put params in order of use [#2]
5c62c7c
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Swap 'authors' -> 'full_authors' and 'abbr_authors' -> 'authors' [#2]
e953108 
This makes the metadata annotations in the Auspice visualization look
much nicer.
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add frequencies panel [#2]
8bef86e 
This is _largely_ copy-pasta-ed from the `measles` repo; the one
significant change is I enabled the frequencies on both the whole
genome and prM-E builds, and I set the `min_date` param to
`2017-01-01`, because virtually all of the post-1927 samples are dated
2017 and later.
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Filter out Chinese travel cases from 2016-ish outbreak [#2]
0557dac
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Copypasta assign-colors.py and associated data from dengue [#2]
6625d78
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Remove old colors file; update config [#2]
84fea9b
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Update color_orderings for YFV [#2]
2ac2f54 
Also small script tweak
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Build colors.tsv dynamically during phylo build {#2}
59999fb
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add CI workflow and configs [#2]
ef81bc9
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add example data [#2]
13a56ae 
This is the full NCBI yellow-fever dataset (taxon ID 11089) as
downloaded on 21 Nov 2024.

CI _could_ work just fine without embedding this data in the repo, but
having a hard-coded example-data file means that we don't depend on
NCBI for successful CI runs.
@genehack genehack mentioned this issue Nov 21, 2024
Open
1 task
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add ingest-to-phylo Github workflow [#2]
917d07c
@genehack genehack linked a pull request Nov 21, 2024 that will close this issue
Open
1 task
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Update README [#2]
f3dad1a
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Clean up old cruft in nextclade workflow [#2]
f1a35a6
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@genehack genehack

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Finish modernization nextstrain/yellow-fever
1 participant
@genehack