Merge pull request #189 from nextstrain/default-profile

ingest: Add `profiles/default` to make `-c1 --ri` unnecessary
nextstrain · Sep 22, 2023 · 8a2314e · 8a2314e
2 parents 4b27179 + 3f3c1f2
commit 8a2314e
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diff --git a/ingest/README.md b/ingest/README.md
@@ -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
 

diff --git a/ingest/profiles/default/config.yaml b/ingest/profiles/default/config.yaml
@@ -0,0 +1,4 @@
+cores: all
+rerun-incomplete: true
+printshellcmds: true
+reason: true