Merged
Conversation
Features: - Filter mutations with JSON file. - Single sample or multiple samples. - Introduction of possible BED files tunning per sample. - New inputsingle.csv file
Pending: - See if write maf can be implemented in filterbatch
Features: - Add mut. profile plotting capabilities. - To do: revise if JSON or TSV output
Features: - Compute trinucleotides from annotated depths matrix - Compute mut. profile using the sample specific trinuc. - Add some specific command line options through modules.config Missing: - Option within matrix computation to adjust to genomic trinuc. counts. - Repeat test with proper depths file.
Features: - Compute mutability for all positions using profile and depths. - Compress and index mutabilities with tabix. Missing: - *Handling of all samples together.* - *Depth files for individual samples and for joined batches.*
Features: - Subsetting MAF module and script. - Oncodrive3D/FML modules updated with meta - Updated mutation matrix creation filter to use subset MAF module. - Added germline and depth thresholds.
Features: - Handle Ns in CONTEXT. - Duplicated positions when expanding the panel. - Define basic test and duplexome test. - Remove unnecessary input.
Features: - Update Oncodrive3d container. - Add error strategy ignore since oncodrive3d failed in the duplexome.
This was
linked to
issues
Jan 9, 2024
Closed
7 tasks
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
I connected the following subworkflows:
and started preparing omega.