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wodanaz
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Assembling_viruses
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Simplify running individual scripts
#32
johnbradley
closed
3 years ago
0
Remove path from filename column in depth/genotype compiler
#31
johnbradley
closed
3 years ago
1
Improve check that user has run setup script
#30
johnbradley
closed
3 years ago
0
Error with pipeline
#29
wodanaz
closed
3 years ago
6
Adds workdir to run-dds-escape-variants.sh
#28
johnbradley
closed
3 years ago
0
Add workdir argument to run-dds-escape-variants.sh
#27
johnbradley
closed
3 years ago
1
improve run-escape-variants.sh help
#26
johnbradley
closed
3 years ago
0
Provide instructions for running individual sbatch scripts
#25
johnbradley
closed
3 years ago
2
Fix help for run-escape-variants
#24
johnbradley
closed
3 years ago
0
Look into containerizing the pipeline
#23
johnbradley
opened
3 years ago
2
Saves GATK step 11 files when necessary
#22
johnbradley
closed
3 years ago
0
Save GATK step 11 output
#21
johnbradley
closed
3 years ago
1
Create escape-variants-pipeline.md
#20
johnbradley
closed
3 years ago
0
Removing fix-merged-bed-positions.sh
#19
wodanaz
closed
3 years ago
3
Improve documentation for escape variants pipeline
#18
johnbradley
closed
3 years ago
1
Add -s flag to run-dds-escape-variants.sh
#17
johnbradley
closed
3 years ago
0
surveillance mode for run-dds-escape-variants.sh
#16
wodanaz
closed
3 years ago
2
Adds script to stage data and run pipeline
#15
johnbradley
closed
3 years ago
6
Fix logdir argument
#14
johnbradley
closed
3 years ago
0
Fix run-escape-variants.sh log directory argument
#13
johnbradley
closed
3 years ago
0
Support for staging data
#12
johnbradley
closed
3 years ago
15
Adds command line arguments for the escape-variant pipeline
#11
johnbradley
closed
3 years ago
0
Add setup-escape-variants.sh script
#10
johnbradley
closed
3 years ago
0
Support running multiple pipelines at once
#9
johnbradley
closed
3 years ago
7
Support rerunning the pipeline
#8
johnbradley
closed
3 years ago
1
Remove duplicated hard coded values
#7
johnbradley
closed
3 years ago
5
Automate consensus sequence generation
#6
johnbradley
closed
3 years ago
7
Adds sbatch scripts for gatk steps
#5
johnbradley
closed
3 years ago
4
Adds sbatch scripts for Escape_Variants.md steps 3-5
#4
johnbradley
closed
3 years ago
1
Better handle one time steps
#3
johnbradley
closed
3 years ago
4
Add all steps in Escape_Variants.md to escape-variant-pipeline
#2
johnbradley
closed
3 years ago
0
Adds first two sbatch scripts for ev pipeline
#1
johnbradley
closed
3 years ago
6
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