CIMAC-CIDC/cidc-ngs-pipeline-api issues and pull requests

#67 - Bump black from 19.10b0 to 24.3.0

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#66 - WES: updating WES pipeline overview (wes.md) and wes_output_API.py to…

Pull Request - State: closed - Opened by lentaing almost 2 years ago

#65 - Removing cohort-report from atacseq_output_API.json

Pull Request - State: closed - Opened by jberg1999 about 2 years ago

#64 - Update readme

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

#63 - Updated pipeline diagram and tools

Pull Request - State: closed - Opened by Aashna01 over 2 years ago

#62 - Updating tcr.md with R packages used.

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

#61 - Update ataqseq.md to match chips-ver1-10

Pull Request - State: closed - Opened by jberg1999 over 2 years ago

#60 - CIDC-1417 Create codeql.yaml

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

#59 - CIDC-0 remove unneeded print

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

#58 - CIDC-1393 fix cnvkit typo

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

#57 - CIDC-1393 remove unneeded WES file

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

#56 - CIDC-1386 bump for WES v3

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

#55 - WES Updates: Updates to the ingestion schema for WES stable version 3.0

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

#54 - CIDC-1218 test on python 3.8 and 9 instead of 7

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#53 - WES: files renamed and removed

Pull Request - State: closed - Opened by lentaing about 3 years ago

#52 - CIDC-1203 remove run_ prefix from MSI file in RNA analysis

Pull Request - State: closed - Opened by scvannost about 3 years ago

#51 - Wes optimize

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

#50 - ATACseq report to key-in on batch_id, not cimac_id

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

#49 - Update to tcr.md to include directions and video link for changing meta.csv

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

#48 - update filter_group for report file

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

#47 - Add pull-request-template

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

#46 - LGTM fixes

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

#45 - ignore.txt -> {id}_error.yaml

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

#44 - Update the output files according to the new chips pipeline

Pull Request - State: closed - Opened by baigal628 over 3 years ago

#43 - Add extra file for enlisting exclusions in WES/RNA

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

#42 - WES tumor-only file update

Pull Request - State: closed - Opened by roshni-b almost 4 years ago

#41 - Add missing msisensor txt extension

Pull Request - State: closed - Opened by roshni-b almost 4 years ago

#40 - update for RIMA json file

Pull Request - State: closed - Opened by Lindky almost 4 years ago

#39 - WES: Adding optional RNA-seq files that support WES's neoantigen pred…

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

#38 - File path changes from Len

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

#37 - Require pre-commit

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

#36 - Add requirement for pre-commit

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

#35 - Remove Travis CI

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

#34 - Create ci.yml GA workflow to replace .travis.yml

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

#33 - Set up pre-commit: generate WES API

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

#32 - Remove center from WES output API

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

#31 - Set travis to Python 3.7

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

#30 - "Rebased" WES update

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

#29 - Prepare for working version of autotemplates

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

#28 - fix images URIs in .md

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

#27 - RIMA workflow img - updated version

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

#26 - WES workflow img

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

#25 - Rename exported output_API.json's

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

#24 - Fix typo and version bump

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

#23 - PyPI version bump

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

#22 - Update MANIFEST.in

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

#21 - Add manifest (and version bump)

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

#20 - Update setup.py

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

#19 - Add back pypi publishing

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

#18 - Wrapping in PyPI deploy-able module

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

#17 - fix rna image link (again!)

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

#16 - TCR pipeline docs

Issue - State: closed - Opened by roshni-b over 4 years ago

#15 - Fix file naming/structure

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

#14 - TCR pipeline documentation

Pull Request - State: closed - Opened by d-s-cohen over 4 years ago

#13 - Fix RNA workflow image link

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

#12 - Chips pipeline description

Pull Request - State: closed - Opened by crazyhottommy over 4 years ago - 3 comments

#11 - Rename level1 from RNA name

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

#10 - Add WES Pipeline Documentation

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

#9 - Pytest for JSON Schema

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

#8 - RNA-seq IMmune Analysis (RIMA) pipeline documentation

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

#7 - Wes

Pull Request - State: closed - Opened by lentaing over 4 years ago - 5 comments

#6 - Filter groups for WES

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

#5 - Filter groups for RNA-seq

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

#4 - Add README

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

#3 - Fix file_purpose permissible values

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

#2 - Add neoantigen-II & xhla to WES

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

#1 - Updates to schema format

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

GitHub / CIMAC-CIDC/cidc-ngs-pipeline-api issues and pull requests