[submodule "workflow/github/gatk-workflows/intel-gatk4-somatic-with-preprocessing"] path = workflow/github/gatk-workflows/intel-gatk4-somatic-with-preprocessing url = https://github.com/gatk-workflows/intel-gatk4-somatic-with-preprocessing [submodule "workflow/github/gatk-workflows/seq-format-validation"] path = workflow/github/gatk-workflows/seq-format-validation url = https://github.com/gatk-workflows/seq-format-validation [submodule "workflow/github/gatk-workflows/intel-gatk3-4-germline-snps-indels"] path = workflow/github/gatk-workflows/intel-gatk3-4-germline-snps-indels url = https://github.com/gatk-workflows/intel-gatk3-4-germline-snps-indels [submodule "workflow/github/gatk-workflows/gatk3-data-processing"] path = workflow/github/gatk-workflows/gatk3-data-processing url = https://github.com/gatk-workflows/gatk3-data-processing [submodule "workflow/github/gatk-workflows/gatk4-data-processing"] path = workflow/github/gatk-workflows/gatk4-data-processing url = https://github.com/gatk-workflows/gatk4-data-processing [submodule "workflow/github/gatk-workflows/intel-gatk4-germline-snps-indels"] path = workflow/github/gatk-workflows/intel-gatk4-germline-snps-indels url = https://github.com/gatk-workflows/intel-gatk4-germline-snps-indels [submodule "workflow/github/gatk-workflows/intel-gatk3-germline-snps-indels"] path = workflow/github/gatk-workflows/intel-gatk3-germline-snps-indels url = https://github.com/gatk-workflows/intel-gatk3-germline-snps-indels [submodule "workflow/github/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels"] path = workflow/github/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels url = https://github.com/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels [submodule "workflow/github/gatk-workflows/gatk4-somatic-with-preprocessing"] path = workflow/github/gatk-workflows/gatk4-somatic-with-preprocessing url = https://github.com/gatk-workflows/gatk4-somatic-with-preprocessing [submodule "workflow/github/gatk-workflows/gatk4-somatic-cnvs"] path = workflow/github/gatk-workflows/gatk4-somatic-cnvs url = https://github.com/gatk-workflows/gatk4-somatic-cnvs [submodule "workflow/github/gatk-workflows/gatk4-somatic-snvs-indels"] path = workflow/github/gatk-workflows/gatk4-somatic-snvs-indels url = https://github.com/gatk-workflows/gatk4-somatic-snvs-indels [submodule "workflow/github/jimmybgammyknee/workflows"] path = workflow/github/jimmybgammyknee/workflows url = https://github.com/jimmybgammyknee/workflows [submodule "workflow/github/biowdl/virus-assembly"] path = workflow/github/biowdl/virus-assembly url = https://github.com/biowdl/virus-assembly [submodule "workflow/github/gatk-workflows/five-dollar-genome-analysis-pipeline"] path = workflow/github/gatk-workflows/five-dollar-genome-analysis-pipeline url = https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline [submodule "workflow/github/biowdl/bam-to-gvcf"] path = workflow/github/biowdl/bam-to-gvcf url = https://github.com/biowdl/bam-to-gvcf [submodule "workflow/github/biowdl/jointgenotyping"] path = workflow/github/biowdl/jointgenotyping url = https://github.com/biowdl/jointgenotyping [submodule "workflow/github/biowdl/ChIP-seq"] path = workflow/github/biowdl/ChIP-seq url = https://github.com/biowdl/ChIP-seq [submodule "workflow/github/gatk-workflows/broad-prod-wgs-germline-snps-indels"] path = workflow/github/gatk-workflows/broad-prod-wgs-germline-snps-indels url = https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels [submodule "workflow/github/biowdl/gams"] path = workflow/github/biowdl/gams url = https://github.com/biowdl/gams [submodule "workflow/github/biowdl/pipeline-template"] path = workflow/github/biowdl/pipeline-template url = https://github.com/biowdl/pipeline-template [submodule "workflow/github/johnmous/ChIPseq"] path = workflow/github/johnmous/ChIPseq url = https://github.com/johnmous/ChIPseq [submodule "workflow/github/biowdl/RNA-seq"] path = workflow/github/biowdl/RNA-seq url = https://github.com/biowdl/RNA-seq [submodule "workflow/github/gatk-workflows/gatk4-germline-snps-indels"] path = workflow/github/gatk-workflows/gatk4-germline-snps-indels url = https://github.com/gatk-workflows/gatk4-germline-snps-indels [submodule "workflow/github/cancerit/BRASS-wdl"] path = workflow/github/cancerit/BRASS-wdl url = https://github.com/cancerit/BRASS-wdl [submodule "workflow/github/biowdl/germline-DNA"] path = workflow/github/biowdl/germline-DNA url = https://github.com/biowdl/germline-DNA [submodule "workflow/github/mkim55/deepvar-wdl"] path = workflow/github/mkim55/deepvar-wdl url = https://github.com/mkim55/deepvar-wdl [submodule "workflow/github/SanderEST/cromwell_wdl"] path = workflow/github/SanderEST/cromwell_wdl url = https://github.com/SanderEST/cromwell_wdl [submodule "workflow/github/Seonwhee-Genome/GATK_WDL"] path = workflow/github/Seonwhee-Genome/GATK_WDL url = https://github.com/Seonwhee-Genome/GATK_WDL [submodule "workflow/github/ottojolanki/kallisto-wdl"] path = workflow/github/ottojolanki/kallisto-wdl url = https://github.com/ottojolanki/kallisto-wdl [submodule "workflow/github/dnanexus-rnd/DeepVariant-GLnexus-WDL"] path = workflow/github/dnanexus-rnd/DeepVariant-GLnexus-WDL url = https://github.com/dnanexus-rnd/DeepVariant-GLnexus-WDL [submodule "workflow/github/broadinstitute/TSCA_firecloud_WDLS"] path = workflow/github/broadinstitute/TSCA_firecloud_WDLS url = https://github.com/broadinstitute/TSCA_firecloud_WDLS [submodule "workflow/github/bgm-cwg/Whole-Genome-Sequencing-Workflow"] path = workflow/github/bgm-cwg/Whole-Genome-Sequencing-Workflow url = https://github.com/bgm-cwg/Whole-Genome-Sequencing-Workflow [submodule "workflow/github/karlrl/mgs_sop"] path = workflow/github/karlrl/mgs_sop url = https://github.com/karlrl/mgs_sop [submodule "workflow/github/omixer/metagenophile"] path = workflow/github/omixer/metagenophile url = https://github.com/omixer/metagenophile [submodule "workflow/github/genomicsITER-developers/wdl"] path = workflow/github/genomicsITER-developers/wdl url = https://github.com/genomicsITER-developers/wdl [submodule "workflow/github/raisok/RNAseq_WDL"] path = workflow/github/raisok/RNAseq_WDL url = https://github.com/raisok/RNAseq_WDL [submodule "workflow/github/camccowan/PacBio-WDL-Tools"] path = workflow/github/camccowan/PacBio-WDL-Tools url = https://github.com/camccowan/PacBio-WDL-Tools [submodule "workflow/github/biowdl/QC"] path = workflow/github/biowdl/QC url = https://github.com/biowdl/QC [submodule "workflow/github/biowdl/tasks"] path = workflow/github/biowdl/tasks url = https://github.com/biowdl/tasks [submodule "workflow/github/manning-lab/wgsaParsrWdl"] path = workflow/github/manning-lab/wgsaParsrWdl url = https://github.com/manning-lab/wgsaParsrWdl [submodule "workflow/github/hongiiv/gatk-workflows"] path = workflow/github/hongiiv/gatk-workflows url = https://github.com/hongiiv/gatk-workflows [submodule "workflow/github/ncsa/MayomicsVC"] path = workflow/github/ncsa/MayomicsVC url = https://github.com/ncsa/MayomicsVC [submodule "workflow/github/antonkulaga/antonkulaga"] path = workflow/github/antonkulaga/antonkulaga url = https://github.com/antonkulaga/antonkulaga [submodule "workflow/github/gatk-workflows/intel-faster-alternative-samples"] path = workflow/github/gatk-workflows/intel-faster-alternative-samples url = https://github.com/gatk-workflows/intel-faster-alternative-samples [submodule "workflow/github/gatk-workflows/seq-format-conversion"] path = workflow/github/gatk-workflows/seq-format-conversion url = https://github.com/gatk-workflows/seq-format-conversion [submodule "workflow/github/biowdl/somatic-variantcalling"] path = workflow/github/biowdl/somatic-variantcalling url = https://github.com/biowdl/somatic-variantcalling [submodule "workflow/github/biowdl/aligning"] path = workflow/github/biowdl/aligning url = https://github.com/biowdl/aligning [submodule "workflow/github/oskarvid/wdl_germline_pipeline"] path = workflow/github/oskarvid/wdl_germline_pipeline url = https://github.com/oskarvid/wdl_germline_pipeline [submodule "workflow/github/jimmybgammyknee/uofaBioWDL"] path = workflow/github/jimmybgammyknee/uofaBioWDL url = https://github.com/jimmybgammyknee/uofaBioWDL [submodule "workflow/github/bgm-cwg/Whole-Exome-Sequencing-Workflow"] path = workflow/github/bgm-cwg/Whole-Exome-Sequencing-Workflow url = https://github.com/bgm-cwg/Whole-Exome-Sequencing-Workflow [submodule "workflow/github/Kurt-Hetrick/WDL"] path = workflow/github/Kurt-Hetrick/WDL url = https://github.com/Kurt-Hetrick/WDL [submodule "workflow/github/manning-lab/saigeWdl"] path = workflow/github/manning-lab/saigeWdl url = https://github.com/manning-lab/saigeWdl [submodule "workflow/github/edawson/firecloud-tools"] path = workflow/github/edawson/firecloud-tools url = https://github.com/edawson/firecloud-tools