Push updates to main - #481
Draft
FerriolCalvet wants to merge 90 commits into
Draft
Conversation
- select the correct gene column - remove '-' as a gene missing: - check if there is an additional ',' at the end
- new container for query independent from dNdS Missing: - container dependencies should be installed but are not found
- Merge remote-tracking branch 'origin/custom-refcds' into feat/dynamic-refcds - add script from intogen repo
- add automatic querying to Ensembl biomart - filter regions based on consensus panel - output dNdS: cv, loc and global - output warning of false splicesites
-not tested
- testing pending
-species and genome were not used
…ts (#439) * Initial plan * feat: add depth-vs-metrics QC module and workflow wiring Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * refactor: remove test-data coupling from optional QC placeholders Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: harden optional input handling for metrics-vs-depth QC Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * style: tighten metrics-vs-depth QC output globs Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: create metrics-vs-depth stub output directory Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: plot and focus the analysis within each gene - sample comparisons are relevant within a gene - comparisons between genes of the same sample are not that relevant - add FIXME for defining command line arguments properly * update depth plots * update depth qcs plot working * exclude subgenic elements from depth qc * cleanup workflow - activate the use of all groups * restrict number of genes plotted to 200 --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> Co-authored-by: FerriolCalvet <ferriolcalvet@gmail.com>
* implement optional gff3 local file * allow local gff3 definition * small suggested update * minor fixes in config * fix bug in processing of non-human genomes
* Initial plan * Add VAF distortion threshold parameter Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/401bf46f-f988-4886-945d-ddca759982d1 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- not tested
- updated profile_all logic
add dynamic RefCDS definition for dNdScv
* remove computation of simple mutdensity_adjusted - omega not working * provide adjusted mutation density to omega - not tested, but should work - NOT CORRECT * rename and reorganize mutdensity files * update adjusted mut density with sample values - add drop duplicates with potential fix * add adjusted mut density variability plots - not tested * fix bug after upstream change * fix error in computation of adjusted mutation density * fix bug in synonymous mut. density selection * add dndsproxy computation * fix dnds proxy computation * update 0 handling and output * run omega preprocessing once * update omega execution to a single case * fix merge remainders * temporary fix coexistent synmutdensity modes - this results in - a correct omega computation (consistent with the current implementation of the method) - the computation of the dnds proxy value that has remained hidden for too long - not tested * fix bugs - tested * mutation densities working - omega still to be recovered * undo all changes in omega * apply suggested from review
* added debuggings * remove channel logs
- add mutdensity sample to interindividual variability - update mutations per cell script (not used)
…ants refactor: uniformize somatic-variant definition across bin scripts
* Initial plan * Apply remaining changes * working hotspot selection groups - pending to apply multiple testing correction * add reporting of more counts - not tested * fix hotspots selection tables * make depths plotting optional * apply review comments --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: FerriolCalvet <ferriolcalvet@gmail.com> Co-authored-by: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
chore: clean up Nextflow selector warnings and dead config
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
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.