Harmonize ingest with pathogen repo guide #35
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As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
As part of conforming to the Pathogen Repo guide https://github.com/nextstrain/pathogen-repo-guide
Match the upload rules in the pathogen-repo-guide https://github.com/nextstrain/pathogen-repo-guide/tree/main/ingest/build-configs/nextstrain-automation
Match pathogen-repo-guide nextstrain/pathogen-repo-guide@d9751bb
j23414
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Changes look good to me!
I left comments on some additional clean up that I missed in nextstrain/zika@cee62cf and was also missed in #34
ingest/Snakefile
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| configfile: "config/config.yaml" | ||
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| configfile: "defaults/config.yaml" | ||
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| send_slack_notifications = config.get("send_slack_notifications", False) |
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Missed this when I was reviewing nextstrain/zika@cee62cf, but this line can be removed since we are no longer sending Slack notifications.
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Good catch! Dropped slack related code and docs in 2e14f00
ingest/Snakefile
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| @@ -57,12 +54,13 @@ rule all: | |||
| _get_all_targets, | |||
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Ditto missed this when I was reviewing nextstrain/zika@cee62cf, but I think the all rule can be simplified to the default targets and the entire _get_all_targets function can be removed.
rule all:
input:
expand(["results/sequences_{serotype}.fasta", "results/metadata_{serotype}.tsv"], serotype=serotypes)
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Ohh, I like the simplified default targets. Fixed in ed1bf1f
Should have been part of #34 Fixed here.
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Description of proposed changes
Harmonize the ingest workflow to match the Pathogen Repo Guide. This may simplify reviewing the E_gene PR and Nextclade rules PR.
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