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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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Update image for chunked scatter.
#224
rhpvorderman
closed
4 years ago
0
Updated resource requirements for the RNA-seq pipeline.
#223
rhpvorderman
closed
4 years ago
0
BIOWDL-474: Add new STAR options for processing rRNA depleted samples.
#222
JasperBoom
closed
4 years ago
0
BIOWDL-472: Update minimumIdentity to correct type and default.
#221
JasperBoom
closed
4 years ago
0
Add bcftools stats and GATK VariantEval
#220
rhpvorderman
closed
4 years ago
0
Fixes for proper MultiQC integration
#219
rhpvorderman
closed
4 years ago
0
BIOWDL-465: Make a number of outputs optional in Picard.
#218
JasperBoom
closed
4 years ago
0
Add necessary options for RNA genotyping to haplotypecaller.
#217
rhpvorderman
closed
4 years ago
0
BIOWDL-453: Fix quotations in samtools sort.
#216
JasperBoom
closed
4 years ago
0
BIOWDL-450: Update/add new tasks to samtools and picard.
#215
JasperBoom
closed
4 years ago
1
BIOWDL-449: Remove dirname command from output folder creation step.
#214
JasperBoom
closed
4 years ago
0
BIOWDL-448: Isoseq3 requires more memory by default.
#213
JasperBoom
closed
4 years ago
0
Add time_minutes runtime_attribute
#212
DavyCats
closed
4 years ago
0
BIOWDL-420: Replace mv command with cp.
#211
JasperBoom
closed
4 years ago
1
Add smoove
#210
cagaser
closed
4 years ago
0
add lumpy/Smoove sv-caller
#209
cagaser
closed
4 years ago
0
Add requirements for fastqc and cutadapt
#208
rhpvorderman
closed
4 years ago
1
Add Star index task
#207
DavyCats
closed
4 years ago
0
Release 3.1.0
#206
rhpvorderman
closed
4 years ago
0
update bwa kit defaults
#205
rhpvorderman
closed
4 years ago
0
BIOWDL-390: Add missing output to parameter_meta.
#204
JasperBoom
closed
4 years ago
0
BIOWDL-390: Make sure stderr log file from Refine is unique and not overwritten.
#203
JasperBoom
closed
4 years ago
0
BIOWDL-390: Fix --min-polya-length argument syntax & add workaround…
#202
JasperBoom
closed
4 years ago
0
BIOWDL-390: Add workaround for glob command in lima.
#201
JasperBoom
closed
4 years ago
0
BIOWDL-390: Add missing backslash.
#200
JasperBoom
closed
4 years ago
0
Update resource requirements
#199
rhpvorderman
closed
4 years ago
0
release v3.0.0
#198
DavyCats
closed
4 years ago
0
Add umi separator
#197
cagaser
closed
4 years ago
0
BIOWDL-390: Add tasks for the PacBio CCS workflow.
#196
JasperBoom
closed
4 years ago
0
make statsPrefix optional for umitools dedup
#195
DavyCats
closed
4 years ago
0
Allow setting --emit-ref-confidence flag on haplotypecaller
#194
rhpvorderman
closed
4 years ago
0
add output mode to haplotypecaller
#193
rhpvorderman
closed
4 years ago
0
Adding tasks for clinical validation.
#192
rhpvorderman
closed
4 years ago
0
add shiny tasks
#191
tomkuipers1402
closed
3 years ago
0
Fix error in bwakit where the output directory was not created.
#190
rhpvorderman
closed
4 years ago
0
fix clever parameter_meta
#189
cagaser
closed
4 years ago
0
Add vt
#188
cagaser
closed
4 years ago
0
fix CombineVariants docker image
#187
DavyCats
closed
4 years ago
0
Add license headers to all the files.
#186
rhpvorderman
closed
4 years ago
0
Combine reorderedGlobbedScatters and scatterRegions. Add pedigree input.
#185
rhpvorderman
closed
4 years ago
0
Changes for the GATK-variantcalling pipeline.
#184
rhpvorderman
closed
4 years ago
0
BIOWDL-395: Add Centrifuge specific Krona task
#183
JasperBoom
closed
4 years ago
0
add umi-tools
#182
DavyCats
closed
4 years ago
0
BIOWDL-331: Fix Centrifuge tests, where sometimes the index files could still not…
#181
JasperBoom
closed
4 years ago
0
BIOWDL-386: Update parameter_meta and fix centrifuge index locating.
#180
JasperBoom
closed
4 years ago
0
add index for commonvariantsites (CollectAllelicounts)
#179
DavyCats
closed
4 years ago
0
BIOWDL-386: Fix issue where Centrifuge could not locate index files.
#178
JasperBoom
closed
4 years ago
0
BIOWDL-386: Fix issue where centrifuge would fail on incorrect paths.
#177
JasperBoom
closed
4 years ago
0
increase default memory for BWA mem
#176
DavyCats
closed
4 years ago
0
make memory configurable in fastqc
#175
DavyCats
closed
4 years ago
0
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