├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── archive ├── README.md ├── magetab_config │ ├── muse.yml │ ├── pindel.yml │ ├── radia.yml │ ├── somatic_sniper.yml │ └── varscan.yml ├── run_config.yaml ├── scripts │ ├── CGHWSI.py │ ├── create_custom_processed_metadata │ ├── docker_check_load.sh │ ├── evaluator.py │ ├── mc3_gatk_wf_gen.py │ ├── mc3_mut.py │ ├── sge_qsub_runworkflow.sh │ ├── synqueue.py │ ├── test_wf_gen.py │ └── vcfToArchive.py ├── tool_data │ ├── bwa_mem_indexes.loc │ ├── cghub_credentials.loc │ └── files │ │ └── STUB_FILE └── workflows │ ├── Galaxy-Workflow-GATK_CGHub_2.ga │ ├── Galaxy-Workflow-GATK_CGHub_3.ga │ ├── Galaxy-Workflow-MC3_Pipeline.ga │ ├── Galaxy-Workflow-MC3_Pipeline_CGHub_DNA.ga │ ├── Galaxy-Workflow-MC3_Pipeline_CGHub_DNA_RNA.ga │ └── Galaxy-Workflow-MC3_Pipeline_Test.ga ├── backup_templates ├── markfiles.cwl~ ├── markfiles.sample_list.tab~ ├── markfiles.sample_list.template~ ├── markfiles.template~ ├── mc3_variant.cwl~ ├── mc3_variant.sample_list.tab~ ├── mc3_variant.sample_list.template~ ├── mc3_variant.template~ ├── mc3_vcf2maf.cwl~ ├── mc3_vcf2maf.sample_list.tab~ ├── mc3_vcf2maf.sample_list.template~ ├── mc3_vcf2maf.template~ ├── mc3_vcf2maf_full.cwl~ ├── mc3_vcf2maf_full.sample_list.tab~ ├── mc3_vcf2maf_full.sample_list.template~ ├── mc3_vcf2maf_full.template~ ├── mc3_vcf_postfilter.cwl~ ├── mc3_vcf_postfilter.sample_list.tab~ ├── mc3_vcf_postfilter.sample_list.template~ ├── mc3_vcf_postfilter.template~ └── sample_list.template~ ├── makeJSON.sh ├── manifest ├── markfiles.cwl ├── mc3_variant.cwl ├── mc3_vcf2maf.cwl ├── mc3_vcf2maf_full.cwl ├── mc3_vcf2maf_full.sample_list.tab ├── mc3_vcf2maf_full.template ├── mc3_vcf_postfilter.cwl ├── refdocs_tree.txt ├── tools └── build-references │ ├── Dockerfile │ └── build_references.cwl ├── tutorial.txt └── utils ├── arraygrep.cwl ├── arraygrep.template ├── backup_templates ├── arraygrep.sample_list.tab ├── arraygrep.sample_list.template~ ├── arraygrep.template~ ├── bai.sample_list.tab ├── bai.sample_list.template~ ├── bai.template~ ├── bgzip.sample_list.tab ├── bgzip.sample_list.template~ ├── bgzip.template~ ├── cat.sample_list.tab ├── cat.sample_list.template~ ├── cat.template~ ├── dict.sample_list.tab ├── dict.sample_list.template~ ├── dict.template~ ├── dirgrep.sample_list.tab ├── dirgrep.sample_list.template~ ├── dirgrep.template~ ├── fai.sample_list.tab ├── fai.sample_list.template~ ├── fai.template~ ├── grep.sample_list.tab ├── grep.sample_list.template~ ├── grep.template~ ├── gzi.sample_list.tab ├── gzi.sample_list.template~ ├── gzi.template~ ├── gzip.sample_list.tab ├── gzip.sample_list.template~ ├── gzip.template~ ├── idx.sample_list.tab ├── idx.sample_list.template~ ├── idx.template~ ├── reference_prep.cwl ├── reference_prep.sample_list.tab ├── reference_prep.sample_list.template~ ├── reference_prep.template ├── reference_prep.template~ ├── tabix.sample_list.tab ├── tabix.sample_list.template~ └── tabix.template~ 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