biowdl tasks issues - Githubissues

biowdl / tasks

A collection of reusable WDL tasks. Category:Other

https://biowdl.github.io/tasks/

MIT License

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issues

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BIOWDL-386: Centrifuge should use -U instead of -1 with single end data.

#174 JasperBoom closed 4 years ago
0
Add bedtools intersect and text to file task.

#173 rhpvorderman closed 4 years ago
0
Add bedtools tasks and add ploidity to haplotypecaller for gender aware variant-calling.

#172 rhpvorderman closed 4 years ago
0
Add tasks for GATK CNV calling

#171 DavyCats closed 4 years ago
0
BIOWDL-380: Update centrifuge task.

#170 JasperBoom closed 4 years ago
0
add parameter_meta

#169 DavyCats closed 4 years ago
0
BIOWDL-379: Fix SQLite error concerning database/disk space being full.

#168 JasperBoom closed 4 years ago
0
Update htseq version

#167 DavyCats closed 4 years ago
0
BIOWDL-371: Update TALON output to align with new version.

#166 JasperBoom closed 4 years ago
0
update scripts submodule

#165 DavyCats closed 4 years ago
0
BIOWDL-369: Update TALON default image to version 4.4.1.

#164 JasperBoom closed 4 years ago
0
update memory for combine gvcfs

#163 rhpvorderman closed 4 years ago
0
Release 2.1.0

#162 rhpvorderman closed 4 years ago
0
BIOWDL-354: Update parameter_meta and TALON task cores.

#161 JasperBoom closed 5 years ago
0
Update TALON to version 4.4

#160 JasperBoom closed 5 years ago
0
add paramter_meta to htseq, cutadapt, collect-columns, stringtie and fastqc

#159 DavyCats closed 5 years ago
0
Changes for RNA pipeline

#158 rhpvorderman closed 5 years ago
0
BIOWDL-327: Update TranscriptClean to version 2.0.2

#157 JasperBoom closed 5 years ago
0
BIOWDL-327: Update TranscriptClean to version 2.0.2

#156 JasperBoom closed 5 years ago
0
Release 2.0.0

#155 rhpvorderman closed 5 years ago
0
Update biowdl-input-converter image

#154 rhpvorderman closed 5 years ago
0
fix small typo

#153 rhpvorderman closed 5 years ago
0
Memory runtime attributes should be Strings not Ints

#152 DavyCats closed 5 years ago
0
Add biowdl-input-converter

#151 rhpvorderman closed 5 years ago
0
Memory should be stated as a string

#150 rhpvorderman closed 5 years ago
0
increase memoryMultiplier for genotypeGVCFs

#149 DavyCats closed 5 years ago
0
BIOWDL-326: Add -k option to minimap2 mapping

#148 JasperBoom closed 5 years ago
0
Add bwakit task

#147 DavyCats closed 5 years ago
0
BIOWDL-308: Add the option for --MD tag to minimap2

#146 JasperBoom closed 5 years ago
0
BIOWDL-261: Update average memory needs for main TALON process

#145 JasperBoom closed 5 years ago
1
Add "SampleConfigToSampleReadgroupLists" task to common.wdl

#144 JasperBoom closed 5 years ago
0
Clean up

#143 DavyCats closed 5 years ago
0
BIOWDL-310: Update TranscriptClean container to version 1.0.8

#142 JasperBoom closed 5 years ago
0
update samtools and htseq-count tasks for supporting more memory efficient counting (e.g. using name sorted bams)

#141 hailiangmei closed 5 years ago
0
Removed "pipefail" from command sections TALON and TranscriptClean

#140 JasperBoom closed 5 years ago
0
BIOWDL-258: Add WDL task for Minimap2

#139 JasperBoom closed 5 years ago
0
BIOWDL-260: Add WDL task for TALON

#138 JasperBoom closed 5 years ago
0
Update fastqsplitter

#137 rhpvorderman closed 5 years ago
0
bigger memory multiplier for filter mutect calls

#136 rhpvorderman closed 5 years ago
1
Update default memory values and CombineVariants to run in Shark

#135 Amfgcp closed 5 years ago
1
BIOWDL-259: Add WDL task for TranscriptClean

#134 JasperBoom closed 5 years ago
1
Simplify cutadapt.

#133 rhpvorderman closed 5 years ago
0
remove default adapter for cutadapt.

#132 rhpvorderman closed 5 years ago
0
Update dockerTag to dockerImage for common.wdl

#131 JasperBoom closed 5 years ago
0
update to run in Shark: memory values and no "-o pipefail"

#130 Amfgcp closed 5 years ago
0
Update picard

#129 rhpvorderman closed 5 years ago
0
M2 gatk4.1.2.0 updates, CombineVariants and Strelka GT modifying

#128 Amfgcp closed 5 years ago
0
Add memory and cores variables to multiqc task.

#127 JasperBoom closed 5 years ago
1
Regions no longer required for several GATK tasks

#126 rhpvorderman closed 5 years ago
0
Add missing index input for panel of normals

#125 Amfgcp closed 5 years ago
1

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