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umccr
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nextflow-stack
AWS stack to run Nextflow pipelines on Batch using shared resources
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Increase initial EBS volume size
#65
scwatts
closed
1 year ago
0
Adjust sash and star-align-nf config for modified stack
#64
scwatts
closed
1 year ago
0
Disable FusionFS/Wave for oncoanalyser
#63
scwatts
closed
1 year ago
0
Bump sash version: 0.1.9 → 0.1.10
#62
scwatts
closed
1 year ago
0
Remove other unneeded run script args
#61
scwatts
closed
1 year ago
0
Restrict local job execution to use with FusionFS
#60
scwatts
closed
1 year ago
0
Remove unneeded oncoanalyser run script argument
#59
scwatts
closed
1 year ago
0
Disable FusionFS for sash
#58
scwatts
closed
1 year ago
0
Bump oncoanalyser version: 0.1.1 → 0.1.2
#57
scwatts
closed
1 year ago
0
Bump sash version: 0.1.6 → 0.1.7
#56
scwatts
closed
1 year ago
0
Bump sash version: 0.1.5 → 0.1.6
#55
scwatts
closed
1 year ago
0
Revert "Bump Nextflow version to 23.04.3"
#54
scwatts
closed
1 year ago
0
Bump Nextflow version to 23.04.3
#53
scwatts
closed
1 year ago
0
Bump Nextflow to 23.04.3
#52
scwatts
closed
1 year ago
0
Fix Nextflow temporary directory paths
#51
scwatts
closed
1 year ago
0
Bump sash version: 0.1.4 → 0.1.5
#50
scwatts
closed
1 year ago
0
Bump sash version: 0.1.3 → 0.1.4
#49
scwatts
closed
1 year ago
0
Bump oncoanalyser version: 0.1.0 → 0.1.1
#48
scwatts
closed
1 year ago
0
Bump sash version: 0.1.1 → 0.1.3
#47
scwatts
closed
1 year ago
0
Append portal run ID to Batch job name
#46
scwatts
closed
1 year ago
0
Adjust SvPrep process config
#45
scwatts
closed
1 year ago
0
Use aws.config filename for templated NF config
#44
scwatts
closed
1 year ago
0
Allow custom oncoanalyser config
#43
scwatts
closed
1 year ago
0
Switch the 16cpu_128gb compute environment to ondemand
#42
scwatts
closed
1 year ago
0
Use switch from SPOT compute environment to ondemand
#41
scwatts
closed
1 year ago
0
Update maxRetries in Nextflow config
#40
scwatts
closed
1 year ago
0
Configure resource ramping for oncoanalyser
#39
scwatts
closed
1 year ago
0
Use git tags as refs in Dockerfile
#38
scwatts
closed
1 year ago
0
Provide metadata information through Batch job parameters
#37
scwatts
closed
1 year ago
6
Add SSM parameter to hold submission lambda ARN
#36
reisingerf
closed
1 year ago
0
Add a new pipeline stack for sash
#35
scwatts
closed
1 year ago
0
Use standard naming for Portal run ID
#34
scwatts
closed
1 year ago
0
Do not upload the .nextflow directory to main analysis destination
#33
scwatts
opened
1 year ago
0
Update oncoanalyser to Pv5 v5.33 alignment branch
#32
scwatts
closed
1 year ago
0
Adjust max vCPUs for Batch job queues
#31
scwatts
closed
1 year ago
3
Bump semver from 6.3.0 to 6.3.1
#30
dependabot[bot]
closed
7 months ago
0
Implement pipeline Batch job submission Lambdas
#29
scwatts
closed
1 year ago
1
Add support for new oncoanalyser run modes
#28
scwatts
closed
1 year ago
0
Bump aws-cdk-lib from 2.73.0 to 2.80.0
#27
dependabot[bot]
closed
7 months ago
0
Use correct instance types for SPOT job queue
#26
scwatts
closed
1 year ago
0
Upgrade Nextflow and FusionFS
#25
scwatts
closed
1 year ago
0
Adjust for ORANGE WTS support in oncoanalyser
#24
scwatts
closed
1 year ago
0
Adjust job definition name template
#23
scwatts
closed
1 year ago
0
Fix several star-align-nf SSM key retrieve functions
#22
scwatts
closed
1 year ago
0
Update HMF data path
#21
scwatts
closed
1 year ago
0
Update output bucket and refactor pipeline stacks
#20
scwatts
closed
1 year ago
3
Update oncoanalyser custom LILAC process selectors
#19
scwatts
closed
1 year ago
0
Allow use of the GRCh38_umccr reference genome in oncoanalyser
#18
scwatts
closed
1 year ago
0
Remove STAR index entry in oncoanalyser config
#17
scwatts
closed
1 year ago
0
Remove unnecessary trailing slash trimming
#16
scwatts
closed
1 year ago
0
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