WDL Pipelines

files required to run WGS alignment pipeline adapted from GATK

Name		Name	Last commit message	Last commit date
alignment		alignment
bashOperations		bashOperations
cnn_variant_wdl		cnn_variant_wdl
cnv_wdl		cnv_wdl
jointGenotyping		jointGenotyping
json		json
mutect2_wdl		mutect2_wdl
.dockstore.yml		.dockstore.yml
.gitignore		.gitignore
AggregatedBamQC.wdl		AggregatedBamQC.wdl
AggregatedBamQCmod.wdl		AggregatedBamQCmod.wdl
Alignment.wdl		Alignment.wdl
Alignment_tasks.wdl		Alignment_tasks.wdl
BamCramConvert.forGitHub.wdl		BamCramConvert.forGitHub.wdl
BamProcessing.wdl		BamProcessing.wdl
BamToCram.wdl		BamToCram.wdl
CombinedClinicalReport.wdl		CombinedClinicalReport.wdl
CombinedClinicalReportModified.wdl		CombinedClinicalReportModified.wdl
DNASeqStructs.wdl		DNASeqStructs.wdl
FastQC.wdl		FastQC.wdl
GATKselectVariants.wdl		GATKselectVariants.wdl
Manta1.6.wdl		Manta1.6.wdl
Mutect_Tumor_Only.Snapashot4.wdl		Mutect_Tumor_Only.Snapashot4.wdl
Pipeline_variantJudgment.wdl		Pipeline_variantJudgment.wdl
Qc.wdl		Qc.wdl
README.md		README.md
RSeQC.wdl		RSeQC.wdl
SNV-GermlineMulti.wdl		SNV-GermlineMulti.wdl
SNV-MultiCaller.wdl		SNV-MultiCaller.wdl
SNVMultiCaller		SNVMultiCaller
STARfusion.wdl		STARfusion.wdl
Samtools_Coverage_MapStats.wdl		Samtools_Coverage_MapStats.wdl
SplitLargeReadGroup.wdl		SplitLargeReadGroup.wdl
Strelka2.wdl		Strelka2.wdl
SvABA.wdl		SvABA.wdl
UnmappedBamToAlignedBam.wdl		UnmappedBamToAlignedBam.wdl
Utilities.wdl		Utilities.wdl
VEP104.wdl		VEP104.wdl
WGS_Germline_Pipeline.wdl		WGS_Germline_Pipeline.wdl
WGS_variant_pipeline_main.wdl		WGS_variant_pipeline_main.wdl
WholeGenomeGermlineSingleSample.wdl		WholeGenomeGermlineSingleSample.wdl
abra2.wdl		abra2.wdl
annotsv.wdl		annotsv.wdl
bcftoolsFilter.wdl		bcftoolsFilter.wdl
blat_runner.wdl		blat_runner.wdl
cnvkit.wdl		cnvkit.wdl
combine_tracks_version_modified.wdl		combine_tracks_version_modified.wdl
downsampling.4.wdl		downsampling.4.wdl
downsampling.5.wdl		downsampling.5.wdl
functotator.wdl		functotator.wdl
gridss_task.wdl		gridss_task.wdl
kallisto-workflow.wdl		kallisto-workflow.wdl
oncokb.wdl		oncokb.wdl
pisces_Germline_parallel.wdl		pisces_Germline_parallel.wdl
pisces_Tumour_parallel.wdl		pisces_Tumour_parallel.wdl
pisces_parallel.wdl		pisces_parallel.wdl
pisces_task.wdl		pisces_task.wdl
run_QC_checks.wdl		run_QC_checks.wdl
run_star.wdl		run_star.wdl
star.wdl		star.wdl
star_fusion_workflow.wdl		star_fusion_workflow.wdl
star_index_generate.wdl		star_index_generate.wdl
test_judgement.wdl		test_judgement.wdl
titan_workflow.wdl		titan_workflow.wdl
vardict.wdl		vardict.wdl
wgsmetrics.wdl		wgsmetrics.wdl

Navigation Menu

Repository files navigation

WDL Pipelines

About

Releases

Packages

Contributors

Languages

Latest commit

History

Folders and files

Repository files navigation

WDL Pipelines

About

Resources

Stars

Watchers

Forks

Releases

Packages

Contributors

Languages