Update DEV_Methyl-Seq with latest from main branch #135
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
- Included Ensembl versions in Updates section of DPPD document - Fixed formatting in reference table - Recreated annotation tables, fixed broken columns - Added locally created databases to reference table - Fixed R version in workflow document R installation instructions - Updated reference table directory in workflow document instructions step #3 - Microbes-related changes: Added microbes to reference table, updated changelog
- Completed refactoring of script and addition of microbial organisms
…tations_vGL-DPPD-7110-A Updating pipeline and workflow for GL_RefAnnotTable-A 1.1.0
- Add software updates to CHANGELOG - Add input and output variables to DPPD document - Prepend species name to output files for non-ENSEMBL reference organisms to make sure it is in the file names - Fix unclear variable names and wording in some functions in the script - Move GO column to the end of the annotation tables when applicable
…tations_vGL-DPPD-7110-A Software version updates, input output variables defined, updated annotation tables
This variable was the same as target_organism, so it was replaced with that variable when necessary.
…tations_vGL-DPPD-7110-A Typo fixes
…tations_vGL-DPPD-7110-A [GL_RefAnnotTable] Installation updates
remove lib path
Store workflow version workflow_code folder name as a variable
Add workflow version variable (for finding install-org-db path) to pipeline documentation
…r workflow_version
…tations_vGL-DPPD-7110-A [GL_RefAnnotTable] Execution fixes
Added command to create the R_libs folder if it doesn't already exist.
Added R_LIB_USER folder creation and SINGULARITY_CACHEDIR setting
Updates to MethylSeq pipeline GL-DPPD-7113
…GL-DPPD-7110-A GeneLab Reference Annotations Pipeline version update from GL-DPPD-7110 to GL-DPPD-7110-A
|
Rebasing DEV_MethylSeq with updates from main branch |
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.
No description provided.