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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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Add missing index input for panel of normals
#125
Amfgcp
closed
5 years ago
1
Add flags to varDict filtering script "var2vcf_paired.pl"
#124
Amfgcp
closed
5 years ago
0
Use compression level 1 in cutadapt.
#123
rhpvorderman
closed
5 years ago
0
Add feature type,idattr and additional attributes to htseq-count task.
#122
rhpvorderman
closed
5 years ago
0
add allow contain
#121
rhpvorderman
closed
5 years ago
0
add task for the chunked-scatter script
#120
DavyCats
closed
5 years ago
0
Some minor changes and small fixes
#119
rhpvorderman
closed
5 years ago
0
DockerImages for all the stuff!
#118
rhpvorderman
closed
5 years ago
0
add panel of normals option to mutect2
#117
Amfgcp
closed
5 years ago
0
Add sv tasks
#116
cagaser
closed
4 years ago
1
Add bowtie
#115
rhpvorderman
closed
5 years ago
0
typo in biopet.wdl
#114
mlin
closed
5 years ago
1
Small fixes
#113
DavyCats
closed
5 years ago
0
Add CNV callers
#112
rhpvorderman
closed
5 years ago
0
simpler md5sum check
#111
rhpvorderman
closed
5 years ago
0
Fixes for germline-DNA pipeline. Removal of structs. Adding outputs.
#110
rhpvorderman
closed
5 years ago
0
md5sums should be Strings not Files
#109
DavyCats
closed
5 years ago
0
Higher memory multipliers
#108
rhpvorderman
closed
5 years ago
0
Allow for unified adapters and contaminations input and set a default.
#107
rhpvorderman
closed
5 years ago
0
Do not extract fastqc zip by default.
#106
rhpvorderman
closed
5 years ago
0
add Collect columns task
#105
DavyCats
closed
5 years ago
0
Updated tasks
#104
cagaser
closed
4 years ago
1
small fixes
#103
DavyCats
closed
5 years ago
0
Fixes for containerizing germline-dna pipeline
#102
rhpvorderman
closed
5 years ago
0
Set additional cpus for vardict
#101
DavyCats
closed
5 years ago
0
add bamFile input to scatterregions
#100
DavyCats
closed
5 years ago
0
Add copy
#99
DavyCats
closed
5 years ago
0
docker added for somatic variantcallers
#98
DavyCats
closed
5 years ago
0
Containerize tasks for RNA-seq
#97
rhpvorderman
closed
5 years ago
0
Work with python slim containers to perform python script tasks.
#96
rhpvorderman
closed
5 years ago
0
some clean up
#95
DavyCats
closed
5 years ago
0
Containerize gffread and cpat
#94
rhpvorderman
closed
5 years ago
0
Public contributions?
#93
multimeric
closed
5 years ago
2
Dockerize GATK. Scattering now works with containers. Tabix another docker image.
#92
rhpvorderman
closed
5 years ago
0
add hisat2 task
#91
DavyCats
closed
5 years ago
0
Move all picard tasks to containers.
#90
rhpvorderman
closed
5 years ago
0
allow for additional annotations to be added into mergecounts output
#89
DavyCats
closed
5 years ago
0
add docker for extract adapters, catadapt and fastqc
#88
DavyCats
closed
5 years ago
0
Saner input for cutadapt
#87
rhpvorderman
closed
5 years ago
0
Add docker for samtools and STAR
#86
DavyCats
closed
5 years ago
0
Make tasks suitable for running against relative paths.
#85
rhpvorderman
closed
5 years ago
0
Allow stringtie to skip novel transcripts
#84
DavyCats
closed
5 years ago
0
add stringtie merge
#83
DavyCats
closed
5 years ago
0
Adapt sane defaults for human analysis.
#82
rhpvorderman
closed
5 years ago
0
add outSAMunmapped to star
#81
DavyCats
closed
5 years ago
0
Add argument for filtering on MAPQ (alignment quality) for View task
#80
johnmous
closed
5 years ago
0
Update stringtie.wdl
#79
DavyCats
closed
5 years ago
0
Macs2 biocontainer
#78
johnmous
closed
5 years ago
0
Add yamltojson task.
#77
rhpvorderman
closed
5 years ago
0
update docs to V0.1
#76
DavyCats
closed
5 years ago
0
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