Metagenomics NF WF Patch update for post-processing WF #153
Conversation
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
Contributor
bnovak32
commented
May 14, 2025
bnovak32
commented
- clean-paths updated to fix bug that removes entire line in front of path to be removed and add better regex for white space
- association table updated
- remove filtered-read-counts which is not generated by Metagenomics pipeline (specific to Amplicon pipeline)
- removed unused parameters
- updated bins/MAGs search to look for zip instead of fasta files
- metagenomics README generation updated
- updated default name/email
- updated to use pathlib instead of os.path, which allows easier directory basename extraction
- fixed naming of directories to match OSDR published data
- removed redundant parent directories
- swapped "_" with " " as in OSDR resource category names
- removed processing info zip content listing
- performance improvement for md5sum generation (maintain and use soft links instead of copying files)
- clean-paths updated to fix bug that removes entire line in front of
path to be removed and add better regex for white space
- association table updated
- remove filtered-read-counts which is not generated by Metagenomics
pipeline (specific to Amplicon pipeline)
- removed unused parameters
- updated bins/MAGs search to look for zip instead of fasta files
- metagenomics README generation updated
- updated default name/email
- updated to use pathlib instead of os.path, which allows easier
directory basename extraction
- fixed naming of directories to match OSDR published data
- removed redundant parent directories
- swapped "_" with " " as in OSDR resource category names
- removed processing info zip content listing
bnovak32
changed the title
|
Updated Validation Report
|
- update README to explicitly list more file names - update Failed-assemblies file to include assay suffix - update version info pulled for KEGG-Decoder (use conda package version) - update curation table name - expand name for "bit" in pipeline software table to make it easier to trace the version
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.