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aofarrel
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clockwork-wdl
WDLization of clockwork
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Update walkthru.wdl
#45
aofarrel
closed
2 months ago
0
Fix decontam counts for cryptic ref
#44
aofarrel
closed
2 months ago
0
Make a Docker image with and without CRyPTIC's minimap2 index
#43
aofarrel
opened
2 months ago
0
Revisit Docker images having not-tarballed reference genomes
#42
aofarrel
opened
2 months ago
0
Hardercode the index and refence files
#41
aofarrel
opened
2 months ago
0
Remove all runtime installation
#40
aofarrel
opened
2 months ago
0
Fix or remove remove contam TSV parsing
#39
aofarrel
opened
2 months ago
1
Final q30 filter doesn't work (but default is too strict anyway)
#38
aofarrel
opened
2 months ago
0
Update to a newer version of clockwork
#37
aofarrel
opened
2 months ago
0
Fix print bugs, fail tiny files in check and decontam task
#36
aofarrel
closed
4 months ago
0
Fix .gz support, better .tar support, out pct_loss
#35
aofarrel
closed
9 months ago
0
Add fastp to combined_decontam, support renaming samples
#34
aofarrel
closed
11 months ago
0
Count reads, rm debug stuff from combined decontamination task
#33
aofarrel
closed
1 year ago
1
Task-level read drop counts
#32
aofarrel
closed
1 year ago
3
Run miniwdl check on push
#31
aofarrel
closed
1 year ago
0
Option to use CDC's decontamination ref instead of CRyPTIC's
#30
aofarrel
closed
1 year ago
0
Add error/status codes to combo decontam task and main variant caller task
#29
aofarrel
closed
1 year ago
2
Variant caller outputs bais, bam output renamed to "bam"
#28
aofarrel
closed
1 year ago
1
New dockers
#27
aofarrel
closed
1 year ago
0
Refprep improvements
#26
aofarrel
closed
1 year ago
1
Create decontamination workflow
#25
aofarrel
closed
1 year ago
1
Ignore bad samples
#24
aofarrel
closed
1 year ago
0
Rename some variables, adjust shellcheck
#23
aofarrel
closed
1 year ago
0
Implement disk type selection
#22
aofarrel
closed
1 year ago
0
Cleanup variant calling
#21
aofarrel
closed
1 year ago
1
Add support for combined decontamination timing out after a period of time
#20
aofarrel
closed
1 year ago
0
Fix shellcheck issues in decontamination tasks
#19
aofarrel
closed
1 year ago
0
Add subsample to decontamination
#18
aofarrel
closed
1 year ago
2
Dupe check
#17
aofarrel
closed
1 year ago
1
Tar fastqs
#16
aofarrel
closed
1 year ago
0
Generating groups of samples that the combined multi-sample task can be scattered upon
#15
aofarrel
closed
1 year ago
1
Make the combined decontamination task able to run on multiple samples at once
#14
aofarrel
closed
1 year ago
1
Combine map_reads and rm_contam into one task
#13
aofarrel
closed
1 year ago
0
Add task combining map_reads and rm_contam tasks to increase efficiency
#12
aofarrel
closed
1 year ago
1
Add var call debugging task
#11
aofarrel
closed
1 year ago
0
Fix sample name
#10
aofarrel
closed
1 year ago
0
Sort by name
#9
aofarrel
closed
2 years ago
0
Variant call debugging files
#8
aofarrel
closed
2 years ago
0
Improve var names
#7
aofarrel
closed
2 years ago
0
Tidy up repository and variable names 🧹
#6
aofarrel
closed
2 years ago
0
Add gvcf task and workflow
#5
aofarrel
closed
2 years ago
0
Tar outputs instead of zipping them, remove some variables
#4
aofarrel
closed
2 years ago
1
Add variant call one sample framework
#3
aofarrel
closed
2 years ago
0
Rename variables
#2
aofarrel
closed
2 years ago
0
Faster zipping experiment
#1
aofarrel
closed
2 years ago
0