Name		Name	Last commit message	Last commit date
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.github		.github
scripts @ 4142daa		scripts @ 4142daa
.gitignore		.gitignore
.gitmodules		.gitmodules
CHANGELOG.md		CHANGELOG.md
CPAT.wdl		CPAT.wdl
LICENSE		LICENSE
README.md		README.md
VERSION		VERSION
bam2fastx.wdl		bam2fastx.wdl
bcftools.wdl		bcftools.wdl
bedtools.wdl		bedtools.wdl
biowdl.wdl		biowdl.wdl
bowtie.wdl		bowtie.wdl
bwa-mem2.wdl		bwa-mem2.wdl
bwa.wdl		bwa.wdl
ccs.wdl		ccs.wdl
centrifuge.wdl		centrifuge.wdl
chunked-scatter.wdl		chunked-scatter.wdl
clever.wdl		clever.wdl
collect-columns.wdl		collect-columns.wdl
common.wdl		common.wdl
cutadapt.wdl		cutadapt.wdl
deconstructsigs.wdl		deconstructsigs.wdl
deepvariant.wdl		deepvariant.wdl
delly.wdl		delly.wdl
duphold.wdl		duphold.wdl
extractSigPredictHRD.wdl		extractSigPredictHRD.wdl
fastp.wdl		fastp.wdl
fastqFilter.wdl		fastqFilter.wdl
fastqc.wdl		fastqc.wdl
fastqsplitter.wdl		fastqsplitter.wdl
fgbio.wdl		fgbio.wdl
flash.wdl		flash.wdl
gatk.wdl		gatk.wdl
gffcompare.wdl		gffcompare.wdl
gffread.wdl		gffread.wdl
gridss.wdl		gridss.wdl
hisat2.wdl		hisat2.wdl
hmftools.wdl		hmftools.wdl
htseq.wdl		htseq.wdl
isoseq3.wdl		isoseq3.wdl
lima.wdl		lima.wdl
macs2.wdl		macs2.wdl
manta.wdl		manta.wdl
minimap2.wdl		minimap2.wdl
multiqc.wdl		multiqc.wdl
nanopack.wdl		nanopack.wdl
ncbi.wdl		ncbi.wdl
pacbio.wdl		pacbio.wdl
pbbam.wdl		pbbam.wdl
pbmm2.wdl		pbmm2.wdl
peach.wdl		peach.wdl
picard.wdl		picard.wdl
prepareShiny.wdl		prepareShiny.wdl
rtg.wdl		rtg.wdl
sambamba.wdl		sambamba.wdl
samtools.wdl		samtools.wdl
seqtk.wdl		seqtk.wdl
smoove.wdl		smoove.wdl
snpeff.wdl		snpeff.wdl
somaticseq.wdl		somaticseq.wdl
spades.wdl		spades.wdl
star.wdl		star.wdl
strelka.wdl		strelka.wdl
stringtie.wdl		stringtie.wdl
survivor.wdl		survivor.wdl
talon.wdl		talon.wdl
transcriptclean.wdl		transcriptclean.wdl
umi-tools.wdl		umi-tools.wdl
umi.wdl		umi.wdl
unicycler.wdl		unicycler.wdl
vardict.wdl		vardict.wdl
vt.wdl		vt.wdl
whatshap.wdl		whatshap.wdl
wisestork.wdl		wisestork.wdl

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Tasks

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

Documentation

Documentation for this repository can be found here.

About

These tasks are part of Biowdl developed by the SASC team at Leiden University Medical Center.

Contact

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

License

biowdl/tasks

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