WDL Pipelines

files required to run WGS alignment pipeline adapted from GATK

Name		Name	Last commit message	Last commit date
Latest commit History 370 Commits
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

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