From 3f3c1f20236b6e0e2818b668dad734fc4719b835 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 22 Sep 2023 18:17:10 +0200 Subject: [PATCH] ingest: Add `profiles/default` to make `-c1 --ri` unnecessary --- ingest/README.md | 8 ++++---- ingest/profiles/default/config.yaml | 4 ++++ 2 files changed, 8 insertions(+), 4 deletions(-) create mode 100644 ingest/profiles/default/config.yaml diff --git a/ingest/README.md b/ingest/README.md index 99084906..8b879d9c 100644 --- 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 new file mode 100644 index 00000000..c69390b8 --- /dev/null +++ b/ingest/profiles/default/config.yaml @@ -0,0 +1,4 @@ +cores: all +rerun-incomplete: true +printshellcmds: true +reason: true