Tasks

This repository contains the WDL task definitions used in the various Biowdl workflows and pipelines.

Documentation

Documentation for this workflow can be found here.

These tasks are part of Biowdl developed by the SASC team.

For any question related to these tasks, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.

Name		Name	Last commit message	Last commit date
Latest commit History 813 Commits
biopet		biopet
scripts @ 56ee741		scripts @ 56ee741
.gitignore		.gitignore
.gitmodules		.gitmodules
.travis.yml		.travis.yml
CPAT.wdl		CPAT.wdl
LICENSE		LICENSE
README.md		README.md
VERSION		VERSION
bioconda.wdl		bioconda.wdl
bowtie.wdl		bowtie.wdl
bwa.wdl		bwa.wdl
centrifuge.wdl		centrifuge.wdl
collect-columns.wdl		collect-columns.wdl
common.wdl		common.wdl
cutadapt.wdl		cutadapt.wdl
fastqc.wdl		fastqc.wdl
flash.wdl		flash.wdl
gatk.wdl		gatk.wdl
gffcompare.wdl		gffcompare.wdl
gffread.wdl		gffread.wdl
hisat2.wdl		hisat2.wdl
htseq.wdl		htseq.wdl
macs2.wdl		macs2.wdl
manta.wdl		manta.wdl
mergecounts.wdl		mergecounts.wdl
multiqc.wdl		multiqc.wdl
ncbi.wdl		ncbi.wdl
picard.wdl		picard.wdl
samtools.wdl		samtools.wdl
seqtk.wdl		seqtk.wdl
somaticseq.wdl		somaticseq.wdl
spades.wdl		spades.wdl
star.wdl		star.wdl
strelka.wdl		strelka.wdl
stringtie.wdl		stringtie.wdl
unicycler.wdl		unicycler.wdl
vardict.wdl		vardict.wdl