mskcc/helix_filters_01 issues and pull requests

#68 - Mutation report

Pull Request - State: open - Opened by svural about 2 years ago

#67 - add_meta_SV_file

Pull Request - State: closed - Opened by nikhil over 2 years ago

#66 - Added cbio fusion to sv converter

Pull Request - State: closed - Opened by nikhil over 2 years ago - 3 comments

#65 - Helix

Pull Request - State: closed - Opened by stevekm over 2 years ago

#64 - added namespaces: ASCN line

Pull Request - State: closed - Opened by svural over 3 years ago

#63 - need to run test cases inside container

Issue - State: closed - Opened by stevekm over 3 years ago - 1 comment
Labels: enhancement, low priority

#62 - added add_msi_status.py and test_add_msi_status.py

Pull Request - State: closed - Opened by svural over 3 years ago

#61 - add CLI args for TMB filter script

Issue - State: open - Opened by stevekm over 3 years ago
Labels: low priority

#60 - Need to exclude some variants from TMB based on Mutation_Status

Issue - State: closed - Opened by stevekm almost 4 years ago - 1 comment

#59 - add TMB variant filter script and test case

Pull Request - State: closed - Opened by stevekm almost 4 years ago - 1 comment

#58 - updated QC and PI report outputs

Issue - State: closed - Opened by stevekm almost 4 years ago - 2 comments

#57 - add MSI Sensor

Issue - State: closed - Opened by stevekm almost 4 years ago - 1 comment

#56 - add TMB calculations

Issue - State: closed - Opened by stevekm almost 4 years ago

#55 - Deprecate CWL & workflow running methods in Makefile

Issue - State: closed - Opened by stevekm about 4 years ago - 1 comment

#54 - Maf clonality

Pull Request - State: closed - Opened by stevekm about 4 years ago

#53 - Fix Facets Suite file headers

Issue - State: closed - Opened by stevekm about 4 years ago - 1 comment

#52 - T af

Pull Request - State: closed - Opened by stevekm about 4 years ago

#51 - Add AF to maf output

Issue - State: closed - Opened by stevekm about 4 years ago - 1 comment

#50 - Add is in impact2

Pull Request - State: closed - Opened by svural about 4 years ago - 1 comment

#49 - multi base mutations

Issue - State: closed - Opened by svural about 4 years ago - 1 comment

#48 - Need test dataset to include in repo

Issue - State: closed - Opened by stevekm about 4 years ago - 2 comments

#47 - start maf_filter.py parity test suite

Pull Request - State: open - Opened by stevekm about 4 years ago - 2 comments

#46 - Added add_is_in_impact.py

Pull Request - State: closed - Opened by svural about 4 years ago - 1 comment

#45 - Need writeup for development protocols

Issue - State: open - Opened by stevekm about 4 years ago

#44 - add OncoKB annotation to maf output

Issue - State: closed - Opened by stevekm about 4 years ago - 3 comments

#43 - Add clonality to maf output

Issue - State: closed - Opened by stevekm about 4 years ago - 1 comment

#42 - Add IMPACT presence to maf output

Issue - State: closed - Opened by stevekm about 4 years ago - 1 comment

#41 - update Makefile

Pull Request - State: closed - Opened by stevekm about 4 years ago

#40 - Maf filter refactor

Pull Request - State: closed - Opened by stevekm about 4 years ago

#39 - Dev

Pull Request - State: closed - Opened by stevekm over 4 years ago

#38 - Add rejected variants output

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#37 - Hook into Dockerhub

Issue - State: closed - Opened by nikhil over 4 years ago

#36 - Add optional command wrapper

Pull Request - State: closed - Opened by nikhil over 4 years ago

#35 - Refactor maf_filter.py to `yield` each filtered row

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#34 - Use parity dataset for testing changes to maf_filter.py script

Issue - State: open - Opened by stevekm over 4 years ago - 1 comment

#33 - Empty string turns into `NA` in `concat-tables.py` script

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#32 - Dev

Pull Request - State: closed - Opened by stevekm over 4 years ago

#31 - Remove CWL workflows

Issue - State: closed - Opened by stevekm over 4 years ago

#30 - Dev

Pull Request - State: closed - Opened by stevekm over 4 years ago

#29 - Update portal data

Pull Request - State: closed - Opened by stevekm over 4 years ago

#28 - add new columns for Facets output

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#27 - rename old data_CNA.scna.txt to data_CNA.txt and replace ILLOGICAL va…

Pull Request - State: closed - Opened by stevekm over 4 years ago

#26 - cBio data_CNA.txt file fails validation

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#25 - 20.06.2

Pull Request - State: closed - Opened by stevekm over 4 years ago

#24 - Concat with comments

Pull Request - State: closed - Opened by stevekm over 4 years ago - 1 comment

#23 - Fix duplicate patient ID outputs

Pull Request - State: closed - Opened by stevekm over 4 years ago

#22 - duplicate patient names

Issue - State: closed - Opened by stevekm over 4 years ago
Labels: bug

#21 - split helix_filters_01 repo into separate cwl and bin repo's

Issue - State: closed - Opened by stevekm over 4 years ago - 2 comments

#20 - Update Facets workflow for new Facets suite release

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#19 - split maf_filter.py script into analysis and cBio Portal

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#18 - Split off Facets workflow

Issue - State: closed - Opened by stevekm over 4 years ago

#17 - Split cBioPortal and analysis workflow

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#16 - Dev

Pull Request - State: closed - Opened by stevekm over 4 years ago

#15 - Figure out why output files are different

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#14 - Need version label embedded in comments

Issue - State: closed - Opened by stevekm over 4 years ago

#13 - Need better method for testing input and output file contents

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#12 - Need unit tests for CWL's

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#11 - Dev

Pull Request - State: closed - Opened by stevekm over 4 years ago

#10 - Feature/concat refactor dev

Pull Request - State: closed - Opened by nikhil over 4 years ago

#9 - Feature/concat refactor

Pull Request - State: closed - Opened by nikhil over 4 years ago - 1 comment

#8 - Add jenkins testing

Issue - State: closed - Opened by nikhil over 4 years ago - 1 comment

#8 - Add jenkins testing

Issue - State: closed - Opened by nikhil over 4 years ago - 1 comment

#7 - Workflows randomly fail with "completed permanentFail"

Issue - State: closed - Opened by stevekm over 4 years ago

#6 - Merge pull request #5 from mskcc/feature/roslin_rename

Pull Request - State: closed - Opened by stevekm over 4 years ago

#5 - Roslin renamed into Argos

Pull Request - State: closed - Opened by nikhil over 4 years ago

#4 - Concat cwl fails when handling listing

Issue - State: closed - Opened by nikhil over 4 years ago - 3 comments

#3 - Warning messages about inline Javascript in put_in_dir.cwl

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

#2 - Feature/add container

Pull Request - State: closed - Opened by allanbolipata over 4 years ago - 1 comment

#1 - "process no longer exists" error message when running helix filter CWL

Issue - State: closed - Opened by stevekm over 4 years ago - 1 comment

GitHub / mskcc/helix_filters_01 issues and pull requests