Deprecate tsv fasta #640
Merged
Deprecate tsv fasta #640
Conversation
This file contains 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
Taepper
force-pushed
the
deprecate-tsv-fasta
branch
5 times, most recently
from
f412967
to
fb2d185
Compare
Taepper
force-pushed
the
deprecate-tsv-fasta
branch
from
a5a86f3
to
e76ceab
Compare
|
This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog. Note that this might contain changes that are on main, but not yet released. Changelog: 0.4.0 (2024-11-14)⚠ BREAKING CHANGES
FeaturesBug Fixes
|
Taepper
force-pushed
the
deprecate-tsv-fasta
branch
3 times, most recently
from
60a13d3
to
9517a28
Compare
fengelniederhammer
requested changes
Nov 14, 2024
| @@ -51,13 +41,7 @@ class PreprocessingConfig { | |||
| std::optional<uint32_t> duckdb_memory_limit_in_g; | |||
| std::optional<std::filesystem::path> lineage_definitions_file; | |||
| std::optional<std::filesystem::path> ndjson_input_filename; | |||
There was a problem hiding this comment.
Can we make this non-optional now?
There was a problem hiding this comment.
If this were non-optional, it would need a default value. Anyways, I would wait for the config refactor for this. Maybe it will resolve this already
testBaseData/test_preprocessing_config_with_overridden_defaults.yaml
Outdated
Show resolved
Hide resolved
Taepper
force-pushed
the
deprecate-tsv-fasta
branch
from
9517a28
to
ac9fda0
Compare
fengelniederhammer
approved these changes
Nov 14, 2024
It is now impossible to specify an input file different from ndjsonInputFilename. An error will be thrown if this variable is not set. resolves #562 BREAKING CHANGE: `metadataInputFile` key in preprocessing config file has been removed. Instead, ndjson files should be used and specified with the `ndjsonInputFilename` option
Taepper
force-pushed
the
deprecate-tsv-fasta
branch
from
ac9fda0
to
383b924
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
resolves #562
Summary
PR Checklist