remote_files: Add support for directly using local cache - #87
Open
joverlee521 wants to merge 1 commit into
Open
joverlee521 wants to merge 1 commit into
joverlee521 wants to merge 1 commit into
Conversation
The Snakemake storage usually checks the existence and revalidates remote files before using the local cache, which can lead to errors when running the workflow offline even if the local cache already exists. This change adds support to directly use the local cache if it exists and bypass the remote file check when 1. the config parameter `use_remote_files` is False 2. the environment variable `NEXTSTRAIN_REMOTE_FILES` is False 3. the workflow is running offline Based on discussions in <nextstrain/public#47> and changes tested in measles repo <nextstrain/measles@60634e2...b238682>
2 of 5 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
The Snakemake storage usually checks the existence and revalidates remote files before using the local cache, which can lead to errors when running the workflow offline even if the local cache already exists.
This change adds support to directly use the local cache if it exists and bypass the remote file check when
use_remote_filesis FalseNEXTSTRAIN_REMOTE_FILESis FalseBased on discussions in nextstrain/public#47 and changes tested in measles repo
nextstrain/measles@60634e2...b238682
Related issue(s)
Part of nextstrain/public#47
Checklist
If adding a script, add an entry for it in the README.