Merged
Conversation
Add lasts preparations for compute depths subworkflow
Features: - Change script name in process annotation to avoid conflicts
…ls-depth-h-f-file
Features: - Comment unnecessary fixed inputs. - Update panel_postprocessing_annotation.py to make it closer to deepCSA - Add possiblity to select assembly - Add utils_context file for accumulating the related functions. - Reduce complexity of panel annotation subworkflow. - Restructure creating panel modules directory. - Minor changes in other modules/subworkflows. - Minor changes in createpanels subworkflow + uncommenting what did not work for Raquel
Features: - Remove # from depths file header - Add meta to filterbed module - Add additional output to capture panels
Features: - Reorganize consequences in panels. - Sort all_samples MAF output. - Add modules to subset TSV to a given BED regions. - Make annotation depths write a file for each sample+allsamples - Trinucleotide module to generate a single file per execution. - Remove unnecessary fixed inputs. - Add more outputs to createpanels subworkflow. - Create new subworkflow for Mutability computations. Remove from mut_profile - Reflect those changes in deepCSA workflow
Features: - Minor change in annotate depths - compute_mutability.py: Remove code that handled all_samples as a particular case, since we merge all the mutations upstream. - modify output channel of annotate depths - Provide sample specific depths to mutability process - Make trinucleotides output channel sample specific - Join depth channel with mutations and profile
Features: - Remove unnecessary parameters from test and default config. - Update oncodrivefml subworkflow for customizable panel. - Minor input changes of oncodrivefml - Add create custom bedfile module. VERY BASIC CODE. TO BE IMPROVED - Update output name in sigprofiler
- Input does not require batch column - Changes in processing of sites before VEP - Change resources in process annotation
Features: - Add mut. number in profile title - Minor changes in panel creation scripts - Clean sample names when loading mut. profile for mutability. - Modify panel_postprocessing script to reduce python computation. - Add mutational profile of all, nonprot, introns, exons - Add all panel outputs to create panels subworkflow
Features: - Add running oncodrivefml only snvs by default - Compute mutability from non-protein affecting profile - Compute oncodrivefml with both computed mutabilities
Collaborator
|
Ongoing testing:
|
Collaborator
|
Combine the processing of the BAM files to compute the depth and the panels+bed files for performing all the downstream analysis together with the actual downstream analysis. This also includes new modules to work on signatures and an improvement of the computations of mutabilities and mutational profile. It is a version that works, but there are still some ongoing tests that are pending. |
FerriolCalvet
deleted the
2-compute-depths-of-all-the-bam-files-samtools-depth-h-f-file
branch
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
2 participants
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.
No description provided.