lilab-bcb/altocumulus issues and pull requests

#76 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 4 months ago

#75 - get task name and share for aws omics

Pull Request - State: closed - Opened by joshua-gould 6 months ago

#74 - Miniwdl taskname

Pull Request - State: closed - Opened by joshua-gould 8 months ago

#73 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#72 - check for empty disk usage (when running workflow using cromwell run)

Pull Request - State: closed - Opened by joshua-gould 10 months ago

#71 - Replace pandas DataFrame.applymap by DataFrame.map

Pull Request - State: closed - Opened by yihming 11 months ago

#70 - removed recursive keyword as it's not needed (and not recognized by all file systems)

Pull Request - State: closed - Opened by joshua-gould 11 months ago

#69 - fix parsing local log file

Pull Request - State: closed - Opened by joshua-gould 11 months ago

#68 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago

#67 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#66 - update docs

Pull Request - State: closed - Opened by yihming over 1 year ago

#65 - Finish up get_task_status command

Pull Request - State: closed - Opened by yihming over 1 year ago

#64 - Task level status

Pull Request - State: closed - Opened by ReshmaRamaiah10 over 1 year ago

#63 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#62 - save monitoring log stats to tsv file for easy parsing

Pull Request - State: closed - Opened by joshua-gould over 1 year ago

#61 - Fix strato commands

Pull Request - State: closed - Opened by yihming over 1 year ago

#60 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#59 - added timing command. pre-commit updates

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

#58 - pre-commit updates

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

#57 - Run a local WDL workflow via Terra

Issue - State: open - Opened by sjfleming almost 2 years ago - 7 comments

#56 - Terra data model

Issue - State: open - Opened by sjfleming almost 2 years ago - 6 comments

#55 - added ability to parse all monitoring logs from a workflow run direct…

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

#54 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago - 3 comments

#53 - Fix issue when uploading tsv format sample sheet without headers

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

#52 - added MANIFEST.in

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

#51 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#50 - iteritems is deprecated in Pandas v1.5.0

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

#49 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#48 - Redesign sample_manager

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

#47 - Don't use nested indexing when doing assignment

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

#46 - Move setup.py stuffs to pyproject.toml

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

#45 - Fixed several bugs

Pull Request - State: closed - Opened by bli25 about 2 years ago

#44 - Added option to write job id to result file

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

#43 - added imports recursively

Pull Request - State: closed - Opened by joshua-gould over 2 years ago - 1 comment

#42 - delete query command

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

#41 - Use tempfile to create intermediate files

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

#40 - Auto workflow dependency fails in some cases

Issue - State: open - Opened by yihming over 2 years ago

#39 - Add upload test

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

#38 - Fixed imports

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

#37 - Query delete

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

#36 - Run pre-commit hooks on all files

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

#35 - add pre-commit hooks

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

#34 - renamed <under checking> to <parsing workflow>

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

#33 - create zip file containing dependencies automatically for local WDLs

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

#32 - Give informative error message for jobs failed before execution

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

#31 - replace nans in workflow name

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

#30 - Bug fix on sample sheet uploading

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

#29 - Added --type option for query

Pull Request - State: closed - Opened by bli25 over 2 years ago

#28 - Improve FASTQ file uploading

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

#27 - Query: Don't print to screen if output file is set

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

#26 - Added query command

Pull Request - State: closed - Opened by bli25 over 2 years ago

#25 - handle duplicate sample

Pull Request - State: closed - Opened by asmariyaz23 over 2 years ago

#24 - Upload fastq folders

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

#23 - Bug fix for temporary files created by `cromwell run` command

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

#22 - Bug fix for `cromwell get_logs` command

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

#21 - Add `-n` option to `cromwell list_jobs` command

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

#20 - List jobs

Pull Request - State: closed - Opened by asmariyaz23 over 2 years ago

#19 - add --profile to upload command; update docs

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

#18 - Make sure float number are written exactly in updated json

Pull Request - State: closed - Opened by bli25 almost 3 years ago

#17 - Dependency

Pull Request - State: closed - Opened by asmariyaz23 almost 3 years ago

#16 - Do not show underlying cloud commands for brevity

Pull Request - State: closed - Opened by yihming almost 3 years ago

#15 - aws profile argument

Pull Request - State: closed - Opened by rocherroche almost 3 years ago

#14 - alto docs

Pull Request - State: closed - Opened by rocherroche almost 3 years ago

#13 - List jobs

Pull Request - State: closed - Opened by rocherroche almost 3 years ago