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

ingest: Add profiles/default to make -c1 --ri unnecessary #189

Merged
merged 1 commit into from
Sep 22, 2023
Merged

ingest: Add profiles/default to make -c1 --ri unnecessary #189

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions ingest/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,19 +10,19 @@ This is the ingest pipeline for mpox virus sequences.
Fetch sequences with

```sh
nextstrain build --cpus 1 . data/sequences.ndjson
nextstrain build . data/sequences.ndjson
```

Run the complete ingest pipeline with

```sh
nextstrain build --cpus 1 .
nextstrain build .
```

This will produce two files (within the `ingest` directory):

- data/metadata.tsv
- data/sequences.fasta
- `data/metadata.tsv`
- `data/sequences.fasta`

Run the complete ingest pipeline and upload results to AWS S3 with

Expand Down
4 changes: 4 additions & 0 deletions ingest/profiles/default/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cores: all
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Changed from 1 to all but I think that's fine.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I don't know why we ever used 1 in the first place

rerun-incomplete: true
printshellcmds: true
reason: true
Comment on lines +2 to +4
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

These options are newly introduced, but seems reasonable to me.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yep, rerun incomplete just avoids an error, it's something almost everyone adds all the time anyways when running builds