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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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WDL Pipelines

files required to run WGS alignment pipeline adapted from GATK

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files required to run alignment pipeline

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