Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / mskcc/access-pipeline issues and pull requests

#262 - Bump certifi from 2019.3.9 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#261 - Bump pillow from 3.4.2 to 9.3.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#260 - Bump joblib from 0.13.2 to 1.2.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#259 - Bump codecov from 2.0.15 to 2.0.16

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#258 - Bump openpyxl from 1.8.6 to 2.4.2

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#257 - Bump reportlab from 3.3.0 to 3.5.55

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#256 - Bump numpy from 1.16.1 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#255 - Bump pypdf2 from 1.26.0 to 1.27.5

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#254 - Bump pillow from 3.4.2 to 9.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#253 - Bump pillow from 3.4.2 to 9.0.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#252 - Update gbcms_params.yaml

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

#251 - Ij/complex genotyping

Pull Request - State: open - Opened by ionox0 about 3 years ago

#250 - Dmp prod/feature/complex variants

Pull Request - State: open - Opened by ionox0 about 3 years ago
Labels: do not merge

#249 - Bump pillow from 3.4.2 to 8.3.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#248 - remove --rm-dups argument

Issue - State: open - Opened by ionox0 over 3 years ago

#247 - Bump pillow from 3.4.2 to 8.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#246 - Sample sheet workflow

Pull Request - State: open - Opened by aef- over 3 years ago - 1 comment

#245 - Donate CWL tool descriptions to community repo?

Issue - State: open - Opened by mr-c over 3 years ago - 2 comments

#244 - Bump pillow from 3.4.2 to 8.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#243 - Update vardict_paired.cwl

Pull Request - State: open - Opened by aef- almost 4 years ago

#242 - Bump pillow from 3.4.2 to 7.1.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#241 - Python3 updates

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

#240 - Beagle Updates

Pull Request - State: closed - Opened by ionox0 almost 4 years ago

#239 - Fix seek error when combining PDFs during QC

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

#238 - Environment issues when building python_tools

Issue - State: open - Opened by aef- over 4 years ago

#237 - textplot library missing

Issue - State: open - Opened by ionox0 over 4 years ago

#236 - TERT promoter mutations not able to be tagged through tag_hotspots

Issue - State: open - Opened by ionox0 over 4 years ago - 1 comment

#235 - vardict not giving variants

Issue - State: open - Opened by ionox0 over 4 years ago

#234 - SV module missing file exception

Issue - State: open - Opened by ionox0 over 4 years ago

#233 - make tag_hotspots compatible with python3

Issue - State: open - Opened by ionox0 over 4 years ago

#232 - missing Library_input and Library_yield from QC title page after recent merge

Issue - State: closed - Opened by ionox0 over 4 years ago - 9 comments

#231 - stricter validation for generate_access_variants_inputs

Issue - State: open - Opened by ionox0 over 4 years ago - 1 comment

#230 - title file all female (F) makes FALSE in qc report

Issue - State: open - Opened by ionox0 over 4 years ago

#229 - TOIL_LSF_ARGS has become a required environment variable

Issue - State: open - Opened by ionox0 over 4 years ago

#228 - Merging of generate_access_variants_inputs.py script

Issue - State: open - Opened by rhshah over 4 years ago
Labels: enhancement

#227 - Premature termination failure

Issue - State: open - Opened by ionox0 over 4 years ago

#225 - CNV inputs generation script should use absolute paths

Issue - State: open - Opened by ionox0 over 4 years ago

#224 - Remove stdout / stderr redirection from CNV workflow steps

Issue - State: open - Opened by ionox0 over 4 years ago

#223 - 1.3.26 plot module insert sizes plot samples duplicated

Issue - State: closed - Opened by ionox0 almost 5 years ago - 4 comments

#222 - New fix to 2x2 rule

Pull Request - State: closed - Opened by maysunh about 5 years ago

#221 - Fix 2x2 rule

Pull Request - State: closed - Opened by maysunh about 5 years ago

#220 - need to include CNV requirements in setup.sh

Issue - State: closed - Opened by ionox0 about 5 years ago - 1 comment

#219 - pipeline_submit: CNV workflow

Issue - State: closed - Opened by rhshah about 5 years ago
Labels: enhancement

#218 - plots_module.r does not support quotes in title file

Issue - State: closed - Opened by ionox0 about 5 years ago - 1 comment

#217 - Bump pillow from 3.4.2 to 6.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#216 - While testing please remove this parameter.

Issue - State: closed - Opened by rhshah about 5 years ago - 1 comment
Labels: refactor

#215 - finished job gets logged repeatedly in debug mode

Issue - State: open - Opened by ionox0 about 5 years ago

#214 - pull fingerprinting hotfix from DMP

Issue - State: closed - Opened by ionox0 about 5 years ago

#213 - WIP initial ACCESS project creation script

Pull Request - State: closed - Opened by ionox0 about 5 years ago

#212 - Organize /work/access

Issue - State: open - Opened by rhshah about 5 years ago - 1 comment
Labels: enhancement

#211 - CondaMultiError: SafetyError

Issue - State: open - Opened by ionox0 about 5 years ago

#210 - Ij/dmp inno variants integration

Pull Request - State: closed - Opened by ionox0 about 5 years ago - 1 comment

#209 - Toil not parsing bjobs -l info for running jobs

Issue - State: open - Opened by ionox0 over 5 years ago

#207 - rabix - Cannot read property "java_8" from undefined

Issue - State: open - Opened by ionox0 over 5 years ago

#206 - .cleanup not found --> ResolveIndirect error

Issue - State: open - Opened by ionox0 over 5 years ago - 12 comments

#205 - can't use cwl step to create empty_dir anymore

Issue - State: open - Opened by ionox0 over 5 years ago - 1 comment
Labels: invalid

#204 - Mmh/fp unexpected matchfix

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#203 - ResolveIndirect

Issue - State: closed - Opened by ionox0 over 5 years ago - 1 comment

#202 - WIP qc changes as per DMP + Mike requests

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#201 - unicode decode / encode errror

Issue - State: closed - Opened by ionox0 over 5 years ago - 6 comments

#199 - need to keep ALL lsf logging

Issue - State: open - Opened by ionox0 over 5 years ago - 1 comment

#198 - upgrade toil to get fix for tmp dir creation

Issue - State: closed - Opened by ionox0 over 5 years ago - 1 comment

#197 - hotspots in normals

Issue - State: closed - Opened by ionox0 over 5 years ago - 2 comments

#196 - remove SLA param (use TOIL_LSF_ARGS instead)

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#195 - fp_config path change and TD threshold for duplex minor contamination

Pull Request - State: closed - Opened by maysunh over 5 years ago - 2 comments

#194 - Toil 3.19 statsandlogging thead has quit

Issue - State: closed - Opened by ionox0 over 5 years ago

#193 - fixes for upgrading to Toil 3.19.0 (no more extraneous tmp dirs!)

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#192 - Mmh/fp unexpected matchfix

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#191 - Mmh/fp unexpected match fix

Pull Request - State: closed - Opened by maysunh over 5 years ago - 1 comment

#190 - test__create_standard_bam_to_collapsed_qc_inputs warning

Issue - State: open - Opened by ionox0 over 5 years ago

#189 - Ij/bqsr plots

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#188 - juno memory warnings

Issue - State: open - Opened by ionox0 over 5 years ago

#187 - use actual machine epsilon to avoid divisionbyzero errors

Issue - State: open - Opened by ionox0 over 5 years ago

#186 - upgrade to Toil 3.20.x

Issue - State: open - Opened by ionox0 over 5 years ago - 1 comment

#185 - save bqsr files with sample IDs as names

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#184 - testing travis for python tests

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#183 - Ij/juno toil upgrade

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#181 - Fix plots_module.r warnings

Issue - State: open - Opened by ionox0 over 5 years ago - 2 comments

#180 - run_params should have two folder for production and test

Issue - State: closed - Opened by rhshah over 5 years ago
Labels: enhancement

#179 - Make an efficient test file

Issue - State: open - Opened by rhshah over 5 years ago
Labels: enhancement, refactor

#178 - Move hard coded references to run_files folder

Issue - State: closed - Opened by rhshah over 5 years ago
Labels: enhancement, refactor

#177 - ACCESS_Filters SettingWithCopyWarning

Issue - State: open - Opened by ionox0 over 5 years ago

#176 - WIP pipeline complete email

Pull Request - State: closed - Opened by ionox0 over 5 years ago - 1 comment

#175 - WIP Manta workflow

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#174 - Waltz error processing read

Issue - State: open - Opened by ionox0 over 5 years ago

#173 - Mmh/feb2019 edits

Pull Request - State: closed - Opened by ionox0 over 5 years ago

#172 - pyup Scheduled daily dependency update on Friday

Pull Request - State: open - Opened by pyup-bot almost 6 years ago
Labels: update

#171 - pyup Scheduled daily dependency update on Thursday

Pull Request - State: closed - Opened by pyup-bot almost 6 years ago - 1 comment
Labels: update

#170 - pyup Scheduled daily dependency update on Wednesday

Pull Request - State: closed - Opened by pyup-bot almost 6 years ago - 1 comment
Labels: update

#169 - pyup Scheduled daily dependency update on Tuesday

Pull Request - State: closed - Opened by pyup-bot almost 6 years ago - 1 comment
Labels: update

#168 - Ij/collapsing subworkflow

Pull Request - State: closed - Opened by ionox0 almost 6 years ago

#166 - pyup Scheduled daily dependency update on Monday

Pull Request - State: closed - Opened by pyup-bot almost 6 years ago - 1 comment
Labels: update

#156 - ACCESS Variants

Pull Request - State: closed - Opened by ionox0 almost 6 years ago

#151 - pyup Scheduled daily dependency update on thursday

Pull Request - State: open - Opened by pyup-bot almost 6 years ago
Labels: update

#106 - ACCESS Filters

Pull Request - State: closed - Opened by maysunh almost 6 years ago

#100 - pyup Scheduled daily dependency update on saturday

Pull Request - State: closed - Opened by pyup-bot almost 6 years ago - 1 comment
Labels: update