-
Notifications
You must be signed in to change notification settings - Fork 19
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.
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
Add B.1 build, downsample B.1 in non-B.1 builds, rename to mpox #171
Commits on Aug 9, 2023
-
Snakefile: remove AUGUR_RECURSION_LIMIT
The AUGUR_RECURSION_LIMIT is set to 10,000 by default since Augur 22.0.0 and the workflow's minimum required Augur version is now 22.2.0¹ ¹ https://github.com/nextstrain/monkeypox/blob/5216a13c407d0e842b40951907c49de6fc6b967a/Snakefile#L5
Configuration menu - View commit details
-
Copy full SHA for 5761c36 - Browse repository at this point
Copy the full SHA 5761c36View commit details
Commits on Aug 11, 2023
-
Merge pull request #170 from nextstrain/remove-augur-recursion-limit
Snakefile: remove AUGUR_RECURSION_LIMIT
Configuration menu - View commit details
-
Copy full SHA for 12ccb42 - Browse repository at this point
Copy the full SHA 12ccb42View commit details
Commits on Aug 22, 2023
-
Move common values to default config, allow partial overrides
Previously, either config_hmpxv1.yaml was used as the default as-is or all required configuration were to be specified via Snakemake CLI options. This resulted in much duplication of configuration across different usages, and the default was never actually used in practice except for in CI out of convenience of not specifying --configfile. Switch to a two-tiered configuration setup with (1) a base "default" tier of common values that can be applied to all workflow usages and (2) a second tier of usage-specific config values which can also partially override Since some required config entries (e.g. build_name) do not share common values across the existing configs, this results in a workflow that is only usable when additional configuration is defined. This will be addressed by subsequent commits.
Configuration menu - View commit details
-
Copy full SHA for 55f7569 - Browse repository at this point
Copy the full SHA 55f7569View commit details -
Copy values from the hmpxv1 configuration since that was the previous default, but change the names to be boilerplate defaults. Add required entries so that: 1. The default config file serves as a reference for all required keys. 2. The workflow can be run by CI without specifying an additional --configfile.
Configuration menu - View commit details
-
Copy full SHA for 4140aff - Browse repository at this point
Copy the full SHA 4140affView commit details -
Configuration menu - View commit details
-
Copy full SHA for fb81750 - Browse repository at this point
Copy the full SHA fb81750View commit details
Commits on Aug 30, 2023
-
Original reasoning by @tsibley in nextstrain/cli@fab709a: Running on push _and_ PRs is often redundant. For PRs, we really care about the putative merge of the PR branch, and that's what "on: pull_request" tests. We typically do not need push-level CI results for PRs. On the other hand, CI results for every push to master are nice to have both as a safety backstop and for the linear chain of CI history it produces (e.g. to debug the impact of external changes on our CI). The primary downside I see is that you can no longer push without opening a PR just to see what CI says, but I think that's an acceptable tradeoff, especially now that draft PRs are a thing. To mitigate this downside, "on: workflow_dispatch" allows CI to be manually dispatched for a specific branch/tag/commit if you _really_ don't want to open even a draft PR. Trimming unnecessary CI jobs reduces the time to completion for CI runs (good for the dev loop) and reduces organization-level job queuing, which can negatively impact the workflows of other repos. Co-authored-by: Thomas Sibley <tsibley@fredhutch.org>
Configuration menu - View commit details
-
Copy full SHA for 00f324e - Browse repository at this point
Copy the full SHA 00f324eView commit details
Commits on Aug 31, 2023
-
Configuration menu - View commit details
-
Copy full SHA for f96fa06 - Browse repository at this point
Copy the full SHA f96fa06View commit details
Commits on Sep 1, 2023
-
git subrepo pull (merge) ingest/vendored
subrepo: subdir: "ingest/vendored" merged: "c97df23" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "c97df23" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
Configuration menu - View commit details
-
Copy full SHA for afeec9c - Browse repository at this point
Copy the full SHA afeec9cView commit details -
Use centralized scripts for NCBI Virus
`fetch-from-ncbi-virus` from the subrepo is a copy of `fetch-from-genbank` with some extra options. Remove the copy in this repo and update references. The supporting scripts `csv-to-ndjson` and `genbank-url` can also be removed.
Configuration menu - View commit details
-
Copy full SHA for 871817b - Browse repository at this point
Copy the full SHA 871817bView commit details
Commits on Sep 5, 2023
-
Configuration menu - View commit details
-
Copy full SHA for b766498 - Browse repository at this point
Copy the full SHA b766498View commit details
Commits on Sep 11, 2023
-
ingest: Switch to NCBI Datasets CLI to fetch data
Replace our custom fetch scripts that uses the NCBI Virus API with the NCBI Datasets CLI commands. NCBI datasets downloads a virus dataset ZIP file that includes a metadata JSON Lines file and a sequences FASTA file. To maintain a record of the single NDJSON file on S3, extract the sequences FASTA file and format the metadata into a TSV file that are parsed into a single NDJSON file using `augur curate passthru`. The metadata TSV is created using the NCBI `dataformat` command so that we do not have to parse the nested JSON lines files ourselves and header fields are renamed to match the previous fields we used for NCBI Virus. The NDJSON file created here no longer includes equivalent fields for "title" or "publication".
Configuration menu - View commit details
-
Copy full SHA for 82ace30 - Browse repository at this point
Copy the full SHA 82ace30View commit details -
Configuration menu - View commit details
-
Copy full SHA for 32eab02 - Browse repository at this point
Copy the full SHA 32eab02View commit details
Commits on Sep 12, 2023
-
Merge pull request #179 from nextstrain/ncbi-datasets-cli
ingest: Switch to NCBI Datasets CLI to fetch data
Configuration menu - View commit details
-
Copy full SHA for fb0d318 - Browse repository at this point
Copy the full SHA fb0d318View commit details -
rebuild-hmpxv1-big: bump memory
Bumping to 68GiB to keep at c5.9xlarge instance since there's some required "headspace" for Batch¹ ¹ https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1674586033950349?thread_ts=1674254476.788549&cid=C01LCTT7JNN
Configuration menu - View commit details
-
Copy full SHA for 5969604 - Browse repository at this point
Copy the full SHA 5969604View commit details
Commits on Sep 15, 2023
-
description: Update "Underlying data" section to NCBI Datasets
This should have been done as a part of #179, but I totally missed that we have this section in the build's description.
Configuration menu - View commit details
-
Copy full SHA for 68190a0 - Browse repository at this point
Copy the full SHA 68190a0View commit details -
Merge pull request #180 from nextstrain/update-description
description: Update "Underlying data" section to NCBI Datasets
Configuration menu - View commit details
-
Copy full SHA for 942c1d0 - Browse repository at this point
Copy the full SHA 942c1d0View commit details
Commits on Sep 20, 2023
-
Allow trial builds through github action
Add a config variable `auspice_prefix` that's prepended to auspice.json And allow setting of that variable in github action submission
Configuration menu - View commit details
-
Copy full SHA for 99eaf2a - Browse repository at this point
Copy the full SHA 99eaf2aView commit details -
Configuration menu - View commit details
-
Copy full SHA for 25e5cfa - Browse repository at this point
Copy the full SHA 25e5cfaView commit details -
Configuration menu - View commit details
-
Copy full SHA for cd969f7 - Browse repository at this point
Copy the full SHA cd969f7View commit details -
Rename builds and sample differently
New names no longer include the deprecated `monkeypox` name New mpxv and mpxv-IIb builds downsample B.1* sequences so that they don't overwhelm the tree Add an mpxv-IIb-B.1 build that contains only B.1* sequences
Configuration menu - View commit details
-
Copy full SHA for b34b076 - Browse repository at this point
Copy the full SHA b34b076View commit details -
Configuration menu - View commit details
-
Copy full SHA for ea5e21b - Browse repository at this point
Copy the full SHA ea5e21bView commit details -
Configuration menu - View commit details
-
Copy full SHA for 5019420 - Browse repository at this point
Copy the full SHA 5019420View commit details -
Configuration menu - View commit details
-
Copy full SHA for bb308a9 - Browse repository at this point
Copy the full SHA bb308a9View commit details -
Configuration menu - View commit details
-
Copy full SHA for d87c2ef - Browse repository at this point
Copy the full SHA d87c2efView commit details -
Configuration menu - View commit details
-
Copy full SHA for c735b6a - Browse repository at this point
Copy the full SHA c735b6aView commit details