updating README, shell script, nextflow pipeline, and R environment #9
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
…ata script to match the new numbering
…e loading conda environment and ensuring download of nextflow
…to message out how many .zip and .gz files and unzipped if any
…ude new R unzipping script, adding .Rprofile and renv/.gitignore
graceakatsu
changed the title
ivichadriana
requested changes
Jun 18, 2025
…ing the optional unzipping script from the nextflow
updating readme slightly to reflect new format of run_pipeline.sh
|
updating pipeline based on conversation (and also after a conversation with kevin from HPC) - both R and python environments should now be working harmoniously, and the pipeline should be able to be successfully run both on HPC and locally :) PR now ready for review! |
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Outdated suggestions cannot be applied.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.
these updates make the environment and pipeline reproducible and able to be run from one shell script.