-
Notifications
You must be signed in to change notification settings - Fork 6
Module/oncokb maf annotation #189
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.
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
Open
johnoooh
wants to merge
18
commits into
develop
Choose a base branch
from
module/oncokb
base: develop
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
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
buehlere
approved these changes
Aug 26, 2025
remove comment
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Outdated suggestions cannot be applied.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.
Adding a oncokb maf annotation module. I created the oncokb folder so we can add other oncokb scripts to it in the future, such as annotate CNV, among others. You need to add a oncokb token for this to work. I tested it locally with mine. Also, the container PR is here mskcc-omics-workflows/containers#27 but the module doesn't currently use this container, it uses a placeholder on my own dockerhub.
feature/<module_name>
for modules, orfeature/<subworkflow_name>
for subworkflows. For modules, if there is a subcommand use:feature/<module_name>/<module_subcommand>
.versions.yml
file.label
.nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity
nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda