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lilab-bcb
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altocumulus
Command line tool for submitting WDL jobs to Terra or Cromwell server.
https://altocumulus.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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[pre-commit.ci] pre-commit autoupdate
#76
pre-commit-ci[bot]
opened
2 months ago
0
get task name and share for aws omics
#75
joshua-gould
closed
4 months ago
0
Miniwdl taskname
#74
joshua-gould
closed
5 months ago
0
[pre-commit.ci] pre-commit autoupdate
#73
pre-commit-ci[bot]
closed
5 months ago
0
check for empty disk usage (when running workflow using cromwell run)
#72
joshua-gould
closed
8 months ago
0
Replace pandas DataFrame.applymap by DataFrame.map
#71
yihming
closed
8 months ago
0
removed recursive keyword as it's not needed (and not recognized by all file systems)
#70
joshua-gould
closed
9 months ago
0
fix parsing local log file
#69
joshua-gould
closed
9 months ago
0
[pre-commit.ci] pre-commit autoupdate
#68
pre-commit-ci[bot]
closed
9 months ago
0
[pre-commit.ci] pre-commit autoupdate
#67
pre-commit-ci[bot]
closed
10 months ago
0
update docs
#66
yihming
closed
1 year ago
0
Finish up get_task_status command
#65
yihming
closed
1 year ago
0
Task level status
#64
ReshmaRamaiah10
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#63
pre-commit-ci[bot]
closed
1 year ago
0
save monitoring log stats to tsv file for easy parsing
#62
joshua-gould
closed
1 year ago
0
Fix strato commands
#61
yihming
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#60
pre-commit-ci[bot]
closed
1 year ago
0
added timing command. pre-commit updates
#59
joshua-gould
closed
1 year ago
0
pre-commit updates
#58
joshua-gould
closed
1 year ago
0
Run a local WDL workflow via Terra
#57
sjfleming
opened
1 year ago
7
Terra data model
#56
sjfleming
opened
1 year ago
6
added ability to parse all monitoring logs from a workflow run direct…
#55
joshua-gould
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#54
pre-commit-ci[bot]
closed
1 year ago
3
Fix issue when uploading tsv format sample sheet without headers
#53
yihming
closed
1 year ago
0
added MANIFEST.in
#52
joshua-gould
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#51
pre-commit-ci[bot]
closed
1 year ago
0
iteritems is deprecated in Pandas v1.5.0
#50
yihming
closed
2 years ago
0
[pre-commit.ci] pre-commit autoupdate
#49
pre-commit-ci[bot]
closed
2 years ago
0
Redesign sample_manager
#48
yihming
closed
2 years ago
0
Don't use nested indexing when doing assignment
#47
yihming
closed
2 years ago
0
Move setup.py stuffs to pyproject.toml
#46
yihming
closed
2 years ago
0
Fixed several bugs
#45
bli25
closed
2 years ago
0
Added option to write job id to result file
#44
joshua-gould
closed
2 years ago
0
added imports recursively
#43
joshua-gould
closed
2 years ago
1
delete query command
#42
joshua-gould
closed
2 years ago
0
Use tempfile to create intermediate files
#41
yihming
closed
2 years ago
0
Auto workflow dependency fails in some cases
#40
yihming
opened
2 years ago
0
Add upload test
#39
joshua-gould
closed
2 years ago
0
Fixed imports
#38
joshua-gould
closed
2 years ago
0
Query delete
#37
joshua-gould
closed
2 years ago
0
Run pre-commit hooks on all files
#36
joshua-gould
closed
2 years ago
0
add pre-commit hooks
#35
joshua-gould
closed
2 years ago
0
renamed <under checking> to <parsing workflow>
#34
joshua-gould
closed
2 years ago
0
create zip file containing dependencies automatically for local WDLs
#33
joshua-gould
closed
2 years ago
0
Give informative error message for jobs failed before execution
#32
yihming
closed
2 years ago
0
replace nans in workflow name
#31
joshua-gould
closed
2 years ago
0
Bug fix on sample sheet uploading
#30
yihming
closed
2 years ago
0
Added --type option for query
#29
bli25
closed
2 years ago
0
Improve FASTQ file uploading
#28
yihming
closed
2 years ago
0
Query: Don't print to screen if output file is set
#27
yihming
closed
2 years ago
0
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