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chanzuckerberg
/
idseq-workflows
Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31
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12
forks
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Catch shell pipeline failures in run_srst2
#43
kislyuk
closed
4 years ago
0
RunSRST2 unconditionally again
#42
mlin
closed
4 years ago
0
switch to a warning for multiple emitted reads from the same cluster
#41
morsecodist
closed
4 years ago
0
Remove dag_branch parameter
#40
kislyuk
closed
4 years ago
0
local driver wdl for short-read-mngs
#39
mlin
closed
4 years ago
1
Fix issues with consensus genome pipeline
#38
tfrcarvalho
closed
4 years ago
0
add gsnap/gsnapl exe detection to host filter
#37
mlin
closed
4 years ago
1
Rename main workflow to short-read-mngs
#35
kislyuk
closed
4 years ago
0
Import idseq-dag contents
#34
kislyuk
closed
4 years ago
3
Rename main workflow to short-read-mngs
#33
kislyuk
closed
4 years ago
3
Fix issues with error reporting
#32
tfrcarvalho
closed
4 years ago
0
upgrade idseq-dag to v4.11.8
#31
morsecodist
closed
4 years ago
0
Begin release github action
#30
kislyuk
closed
4 years ago
0
remove minDepth param for pileup and nonessential steps
#29
katrinakalantar
closed
4 years ago
0
Add "no reads left" errors
#28
tfrcarvalho
closed
4 years ago
0
Simplify CG docker image and update a few packages
#27
tfrcarvalho
closed
4 years ago
0
Update SwarmContainer path
#26
kislyuk
closed
4 years ago
0
Add optional usegsnapl option
#25
morsecodist
closed
4 years ago
3
Create CONTRIBUTING.md
#24
kislyuk
closed
4 years ago
0
add miniwdl download cache cleaner script to main docker
#23
mlin
closed
4 years ago
0
add host_filter RunStar test case using smaller ERCC database
#22
mlin
closed
4 years ago
0
Add consensus genome workflow
#21
tfrcarvalho
closed
4 years ago
2
Readd STARlong
#20
morsecodist
closed
4 years ago
0
Switch to public references
#19
morsecodist
closed
4 years ago
0
task unit skeletons for postprocess & experimental
#18
mlin
closed
4 years ago
0
enable more task tests by letting miniwdl handle small/medium S3 downloads
#17
mlin
closed
4 years ago
0
Keep curl in idseq-wdl image
#16
kislyuk
closed
4 years ago
0
Emit unique_unidentified_fa in NHA
#15
kislyuk
closed
4 years ago
1
Restore index_dir_suffix
#14
kislyuk
closed
4 years ago
0
run tests using just-built docker image
#13
mlin
closed
4 years ago
0
Bump idseq-dag to 4.11.3
#12
morsecodist
closed
4 years ago
0
Add rapsearch2 to docker image
#11
morsecodist
closed
4 years ago
0
host_filter task unit tests (auto-generated)
#10
mlin
closed
4 years ago
5
build docker image through GitHub Actions+Packages
#9
mlin
closed
4 years ago
1
Add main workflow Dockerfile
#8
kislyuk
closed
4 years ago
0
add test cases for maximum e-value filter on alignment results
#7
katrinakalantar
opened
4 years ago
0
Simplify WDL input
#6
kislyuk
closed
4 years ago
0
start phasing out aws_region and deployment_env inputs
#5
mlin
closed
4 years ago
5
basic host_filter test
#4
mlin
closed
4 years ago
1
Port workflow conditional logic from idseq-web
#3
kislyuk
closed
4 years ago
1
run `miniwdl check` through pre-commit
#2
mlin
closed
4 years ago
0
Begin IDseq WDL workflows
#1
kislyuk
closed
4 years ago
0
Running test locally fail
#36
eamanu
opened
4 years ago
1
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