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biowdl
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tasks
A collection of reusable WDL tasks. Category:Other
https://biowdl.github.io/tasks/
MIT License
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Use softlink instead of hardlinks for centrifuge
#324
Redmar-van-den-Berg
closed
1 year ago
0
bwa index wrong
#323
lihaicheng7003
closed
1 year ago
0
add a task for fastq-filter
#322
DavyCats
closed
1 year ago
0
Add revcomp flag to cutadapt
#321
DavyCats
closed
1 year ago
0
Update FastQC and cutadapt
#320
rhpvorderman
closed
1 year ago
0
Release 5.1.0
#319
rhpvorderman
closed
1 year ago
0
Add inputs for hfmtool's purple "shallow mode"
#318
DavyCats
closed
1 year ago
0
add some options to disable filters in fastp
#317
DavyCats
closed
1 year ago
0
Add fastp and picard CollectInsertSizeMetrics
#316
DavyCats
closed
1 year ago
0
Allow a custom separator char in tagUmi
#315
rhpvorderman
closed
1 year ago
0
Fix arg space
#314
johnmous
closed
1 year ago
0
Add a number of macs2 flags so we can adhere to Encode
#313
johnmous
closed
1 year ago
0
add various tasks for somatic SV calling
#312
DavyCats
closed
1 year ago
1
Unzip/gzip
#311
mmterpstra
closed
1 year ago
1
Add target file input to samtools view
#310
rhpvorderman
closed
1 year ago
1
Fallback to copying when hardlinking does not work
#309
rhpvorderman
closed
1 year ago
0
Adjust gridss SV typing task to also filter duplicate records
#308
DavyCats
closed
1 year ago
0
update survivor version
#307
DavyCats
closed
1 year ago
1
Add bwa index and a combined fai + dict index task.
#306
rhpvorderman
closed
1 year ago
1
Use gebibytes instead of gigabytes
#305
rhpvorderman
closed
2 years ago
0
Performance changes for WGSinCancerDiagnostics
#304
DavyCats
closed
2 years ago
0
Updates for WGSinCancerDiagnostics
#303
DavyCats
closed
2 years ago
0
Add GT to gridss results in AnnotateSvTypes
#302
DavyCats
closed
2 years ago
0
Add a task to add SVTYPE annotations to GRIDSS results
#301
DavyCats
closed
2 years ago
0
run tabix if vcf index is missing in gridss
#300
DavyCats
closed
2 years ago
0
Add format parameter to macs2
#299
rhpvorderman
closed
2 years ago
0
Updates for WGSinCancerDiagnostics
#298
DavyCats
closed
2 years ago
0
Add picard dedup
#297
cagaser
closed
2 years ago
1
Speed up integration testing.
#296
rhpvorderman
closed
2 years ago
0
Add sample position in array task, update parameter_meta for macs2.
#295
rhpvorderman
closed
2 years ago
0
Samtools add optional index file as input
#294
cagaser
closed
2 years ago
1
bump scatterregions container
#293
leipzig
closed
2 years ago
0
Famm run
#292
cagaser
closed
2 years ago
0
force co-localization of indexes with their targets
#291
mr-c
closed
2 years ago
11
Patch tasks
#290
cagaser
closed
3 years ago
0
Add runtime memory
#289
cagaser
closed
3 years ago
0
Release 5.0.0
#288
cagaser
closed
3 years ago
0
Fix task ci
#287
cagaser
closed
3 years ago
0
update CHANGELOG and scripts
#286
cagaser
closed
3 years ago
0
Update CPAT to version 3.0.4
#285
DavyCats
closed
3 years ago
0
Task issue 281
#284
cagaser
closed
3 years ago
0
Set defaults for boolean values
#283
rhpvorderman
closed
3 years ago
1
Use of placeholder with optional value in spades.wdl
#282
jdidion
closed
3 years ago
1
Invalid placeholder option values in survivor.wdl
#281
jdidion
closed
3 years ago
1
Add mkdir line to samtools fastq.
#280
JasperBoom
closed
3 years ago
3
BIOWDL-531: Update tool versions.
#279
JasperBoom
closed
3 years ago
0
Move pacbio-merge image to quay.io
#278
Redmar-van-den-Berg
closed
3 years ago
0
fix some runtime settings
#277
DavyCats
closed
3 years ago
0
Fix memory values.
#276
JasperBoom
closed
3 years ago
0
Make referenceAnnotation optional in GffCompare and add minimumCoverage for stringtie
#275
DavyCats
closed
3 years ago
0
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