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Sydney-Informatics-Hub
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Germline-StructuralV-nf
Germline structural variant calling pipeline for short read WGS datasets
GNU General Public License v3.0
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Remove harcoded `GRCh38` version for `AnnotSv`
#76
juanesarango
closed
3 weeks ago
1
Add Picard ValidateSamFile module
#75
calizilla
opened
11 months ago
0
Final release
#74
georgiesamaha
closed
11 months ago
0
Final release of workflow v1.0.0
#73
georgiesamaha
closed
11 months ago
0
Feature request: check bam index age or presence and reindex if needed
#72
georgiesamaha
opened
11 months ago
0
Read samplesheet via column position not header label
#71
calizilla
opened
11 months ago
0
Add additional checks to check_cohort.nf
#70
calizilla
opened
11 months ago
0
Reference fasta is staged by tiddit module but not used
#69
calizilla
opened
11 months ago
0
change nextflow.config & hashed beforeScript in gadi.config
#68
chlu0571
closed
11 months ago
0
Fixed *.config & queue in PBS_gadi_runpipeline.sh
#67
chlu0571
closed
11 months ago
0
Fix issue #65: mix up of pbs and gadi parameters
#66
georgiesamaha
closed
11 months ago
0
Inconsistent parameter definition and application for gadi account
#65
georgiesamaha
closed
11 months ago
1
pullContainers.sh not utilising specified cachedir
#64
calizilla
closed
11 months ago
2
Pre-download images
#63
calizilla
closed
11 months ago
2
Add KSU usage estimates for resource management
#62
calizilla
closed
11 months ago
0
Finalise Tower integration with scalable run on Gadi
#61
georgiesamaha
closed
1 year ago
0
Tower integration
#60
georgiesamaha
closed
1 year ago
2
Gadi local jobs failing to access 10Gb memory
#59
georgiesamaha
closed
1 year ago
0
Add gdata to gadi config
#58
georgiesamaha
closed
1 year ago
0
Add Tower.yaml for report exposure on interface
#57
georgiesamaha
closed
1 year ago
2
Tower Gadi implementation
#56
georgiesamaha
closed
1 year ago
0
Update gadi.config
#55
georgiesamaha
closed
1 year ago
0
Remove beforeScript
#54
georgiesamaha
closed
1 year ago
0
Fix gadi.config beforeScript
#53
georgiesamaha
closed
1 year ago
0
Update nextflow_schema.json
#52
georgiesamaha
closed
1 year ago
0
Update nextflow_schema.json for tower
#51
georgiesamaha
closed
1 year ago
0
Fix indenting of nextflow.config
#50
georgiesamaha
closed
1 year ago
0
fix manta container, fix pbs script
#49
georgiesamaha
closed
1 year ago
0
tower implementation fixes
#48
georgiesamaha
closed
1 year ago
0
Fix parameters for tower
#47
georgiesamaha
closed
1 year ago
0
Tidy up parameters for tower integration
#46
georgiesamaha
closed
1 year ago
0
remove tower.yml
#45
georgiesamaha
closed
1 year ago
0
Add tower.yml and params.json for tower configurations
#44
georgiesamaha
closed
1 year ago
0
nextflow_schema.json
#43
georgiesamaha
closed
1 year ago
0
Flexible customisation options
#42
georgiesamaha
closed
1 year ago
0
Create trace timestamp
#41
georgiesamaha
closed
1 year ago
0
Apply additional flags to AnnotSV
#40
georgiesamaha
closed
1 year ago
0
Flexible AnnotSV annotation mode
#39
georgiesamaha
closed
1 year ago
0
run small jobs with small slurm allocation
#38
SarahBeecroft
closed
1 year ago
0
run small jobs with local executor
#37
SarahBeecroft
closed
1 year ago
0
include specific timings for jobs
#36
SarahBeecroft
closed
1 year ago
0
Add CNV module
#35
georgiesamaha
closed
1 year ago
1
Annotation type flag for AnnotSV
#34
georgiesamaha
closed
1 year ago
0
-SVminSize flag for AnnotSV
#33
georgiesamaha
closed
1 year ago
0
add newer tidbit container
#32
SarahBeecroft
closed
1 year ago
0
remove dummy account variable
#31
SarahBeecroft
closed
1 year ago
0
Pipeline feedback
#30
gavinmonahan
closed
12 months ago
5
added gadi config
#29
georgiesamaha
closed
1 year ago
0
added setonix.config to this file
#28
SarahBeecroft
closed
1 year ago
0
Portability testing @ Pawsey Setonix
#27
georgiesamaha
closed
1 year ago
0
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