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biowdl
/
tasks
A collection of reusable WDL tasks. Category:Other
https://biowdl.github.io/tasks/
MIT License
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Add new multi package container with umi and samtools
#274
cagaser
closed
3 years ago
0
Add new multi package container with umi and samtools
#273
cagaser
closed
3 years ago
0
Umi tools add tmp dir
#272
cagaser
closed
3 years ago
0
Add duphold
#271
cagaser
closed
3 years ago
0
escape sequences in regex
#270
mlin
opened
3 years ago
2
add tasks to create files for DGE analysis
#269
tomkuipers1402
closed
3 years ago
0
Use github actions CI
#268
rhpvorderman
closed
3 years ago
0
downgrade stringtie and fix size call in gffread
#267
DavyCats
closed
3 years ago
0
BIOWDL-532: Apply multiple fixes for PacBio pipeline.
#266
JasperBoom
closed
3 years ago
0
BIOWDL-528: Update version of tools to match new version in workflows.
#265
JasperBoom
closed
3 years ago
0
Add parameter meta
#264
Redmar-van-den-Berg
closed
3 years ago
0
Gvcf index
#263
Redmar-van-den-Berg
closed
3 years ago
1
BIOWDL-524: Add parameter_meta outputs.
#262
JasperBoom
closed
3 years ago
4
BIOWDL-521: Update tasks to a uniform layout/structure.
#261
JasperBoom
closed
3 years ago
0
Fix bugs in tasks for Deepvariant and WhatsHap
#260
Redmar-van-den-Berg
closed
3 years ago
0
Update parameter meta
#259
Redmar-van-den-Berg
closed
3 years ago
0
Update to CCS version 5
#258
Redmar-van-den-Berg
closed
3 years ago
0
bcftools: add tmpDir input to specify temporary directory when sorting.
#257
cagaser
closed
3 years ago
0
Optional indexing
#256
cagaser
closed
3 years ago
0
Contains 2 new tasks for creating dgeAnalysis input files
#255
tomkuipers1402
closed
3 years ago
0
Pacbio variantcalling
#254
Redmar-van-den-Berg
closed
3 years ago
0
BIOWDL-499: Update parameter_meta.
#253
JasperBoom
closed
3 years ago
0
Add parameter meta for threads
#252
Redmar-van-den-Berg
closed
3 years ago
0
BIOWDL-516: Remove metrics file.
#251
JasperBoom
closed
4 years ago
0
BIOWDL-499: Add NanoQC and NanoPlot.
#250
JasperBoom
closed
4 years ago
0
BIOWDL-512: Add timeMinutes to Classify.
#249
JasperBoom
closed
4 years ago
0
Upddate collect-columns
#248
DavyCats
closed
4 years ago
0
Optional indexing
#247
cagaser
closed
4 years ago
0
Update survivor
#246
cagaser
closed
4 years ago
0
Bcftools seperate indexing and expand bcftools view
#245
cagaser
closed
4 years ago
0
Add option to ignore masked reference to VT
#244
Redmar-van-den-Berg
closed
4 years ago
0
Bcftools: added annotation and sorting
#243
cagaser
closed
4 years ago
0
add parameter_meta for SVcalling.gridss.jvmHeapSizeGb
#242
cagaser
closed
4 years ago
0
Gridss
#241
cagaser
closed
4 years ago
0
BIOWDL-487: Remove globs from lima outputs.
#240
JasperBoom
closed
4 years ago
1
BIOWDL-487: Add pacbio bam2fastx tool.
#239
JasperBoom
closed
4 years ago
0
Make intervals optional for GenotypeGVCFs
#238
Redmar-van-den-Berg
closed
4 years ago
0
Release 4.0.0
#237
DavyCats
closed
4 years ago
0
add gridss task
#236
DavyCats
closed
4 years ago
0
Last tweaks before release
#235
rhpvorderman
closed
4 years ago
0
Add bwa-mem2 task.
#234
rhpvorderman
closed
4 years ago
1
Increase the number of sorting threads to prevent pipe blocks in aligners.
#233
rhpvorderman
closed
4 years ago
0
BIOWDL-487: Update output names for the first set of tasks.
#232
JasperBoom
closed
4 years ago
0
Update images
#231
rhpvorderman
closed
4 years ago
0
Better performance by using bam compression level 1 in star. Samtools controls to hisat.
#230
rhpvorderman
closed
4 years ago
0
Add vep
#229
cagaser
closed
3 years ago
0
Use htsjdk inflaters and deflaters for markduplicates
#228
rhpvorderman
closed
4 years ago
0
Update resource requirements for WGS DNA pipelines.
#227
rhpvorderman
closed
4 years ago
0
BIOWDL-426: Add new tasks to talon.
#226
JasperBoom
closed
4 years ago
0
Add pbmm2, the PacBio wrapper for minimap2
#225
Redmar-van-den-Berg
closed
4 years ago
0
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