Potential Feature: Snakemake workflow #193
Open
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
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Outdated suggestions cannot be applied.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.
Hello! I tried to reach out to gauge interest for this on gitter, but thought I'd might as well submit this pull request. I needed to run a large batch of samples and wanted to efficiently utilize our compute cluster. This PR adds a simple workflow to run through (what I understand to be) the typical first steps of MICOM.
This is all described in
workflow_README.md, but in short, it has two stages controlled by a config parameter.--config stage=tradeoff: this runs MICOM's tradeoff determination step, submitting each sample as its own job. When all complete, it combines the results into a tradeoff.csv file and generates the tradeoff plot.--config stage=grow: this runs MICOM's growth step, submitting each sample as its own job. When all complete, these get merged into a singlegrowth.zipfor downstream use.Let me know if this is of interest to your team; happy to adjust this as needed.