Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feature: subworkflow for isolate genomes #127

Open
wants to merge 3 commits into
base: master
Choose a base branch
from
Open

feature: subworkflow for isolate genomes #127

wants to merge 3 commits into from

Conversation

franciscozorrilla
Copy link
Owner

@franciscozorrilla franciscozorrilla commented Jun 9, 2023 •
edited
Loading

🦠 Isolate genomes subworkflow 🔦

Adding support for isolate genome assembly in the next version of metaGEM 💎

🐍 Snakefile tasks

  • create shovill rule for dealing with isolate assembly data
  • create dRep rule for derelplicating megahit assembly, metaGEM-reassembled bin, and shovill output to select best genome
  • create helper rule to populate drep input from corresponding input subfolders

🔨 Additional modifications for full integration/support

  • metaGEM.sh: add options + support for new tasks
  • config.yaml: add params used in new tasks
  • config readme file: add new perl environment for shovill (to also include prokka, roary, etc.), dRep could go in main metaGEM env
  • conda recipe: update
  • main readme file: text and eventually figure

@franciscozorrilla
feature: add shovill rule to Snakefile
7452739 
add shovill rule to Snakefile for dealing with isolate assembly data. will also need to make additions/changes to
* metaGEM.sh: add flag/option to support new task
* config.yaml: add params used in task
* readme file: text and eventually figure
@franciscozorrilla franciscozorrilla self-assigned this Jun 9, 2023
@franciscozorrilla franciscozorrilla added enhancement New feature or request method Novel or alternative conceptual method labels Jun 9, 2023
@franciscozorrilla
Update Snakefile
23fa499 
remove unnecessary code and move shovill rule up to a more appropriate place in the Snakefile
@franciscozorrilla
faet: add new drep_isolate rule
52ae545
@franciscozorrilla franciscozorrilla changed the title feature: add shovill support for metaGEM feature: subworkflow for isolate genomes Jun 9, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees

@franciscozorrilla franciscozorrilla

Labels
enhancement New feature or request method Novel or alternative conceptual method
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@franciscozorrilla