MobiDL - tasks

MobiDL - tasks is a collection of tools wrapped in WDL to be used in any WDL pipelines.

How to use ?

You can use this module as a submodule in another repository.

cd MyWorkflow
git submodule add [email protected]:MobiDL/tasks.git
git config --global diff.submodule log
git config status.submodulesummary 1

git submodule update --remote tasks

Name		Name	Last commit message	Last commit date
Latest commit History 502 Commits
CHANGELOG.md		CHANGELOG.md
GATK4.wdl		GATK4.wdl
LICENSE		LICENSE
README.md		README.md
TOOLS.md		TOOLS.md
achab.wdl		achab.wdl
anacore_utils.wdl		anacore_utils.wdl
annovarForMpa.wdl		annovarForMpa.wdl
bcftools.wdl		bcftools.wdl
bedtools.wdl		bedtools.wdl
bgzip.wdl		bgzip.wdl
bwa.wdl		bwa.wdl
clair.wdl		clair.wdl
clair3.wdl		clair3.wdl
crumble.wdl		crumble.wdl
cutadapt.wdl		cutadapt.wdl
dwgsim.wdl		dwgsim.wdl
fastp.wdl		fastp.wdl
fastqc.wdl		fastqc.wdl
longshot.wdl		longshot.wdl
minimap2.wdl		minimap2.wdl
mpa.wdl		mpa.wdl
multiqc.wdl		multiqc.wdl
nanoplot.wdl		nanoplot.wdl
nanorepeat.wdl		nanorepeat.wdl
nanovar.wdl		nanovar.wdl
phenolyzer.wdl		phenolyzer.wdl
qualimap.wdl		qualimap.wdl
regtools.wdl		regtools.wdl
rsync.wdl		rsync.wdl
rtg.wdl		rtg.wdl
sambamba.wdl		sambamba.wdl
samtools.wdl		samtools.wdl
sed.wdl		sed.wdl
seqkit.wdl		seqkit.wdl
snpEff.wdl		snpEff.wdl
star.wdl		star.wdl
tabix.wdl		tabix.wdl
utilities.wdl		utilities.wdl
vardict-java.wdl		vardict-java.wdl
vep.wdl		vep.wdl