├── .github ├── PULL_REQUEST_TEMPLATE.md ├── scripts │ └── workflow_to_docker_table.py └── workflows │ ├── sync_pr_template.yml │ └── update_docker_tables.yml ├── .gitignore ├── .gitmodules ├── README.md ├── docs ├── SOMATIC_SNV_BENCHMARK.md ├── dockers_consensus.md ├── dockers_somatic.md ├── echtvar_gnomad_annotation.md ├── interval_preparation_walkthrough.md ├── kfdrc-consensus-calling.md ├── kfdrc_amplicon_architect.md ├── kfdrc_annotation_wf.md ├── kfdrc_gatk_cnv_somatic_pair_wf.md ├── kfdrc_gatk_create_cnv_pon_wf.md ├── kfdrc_lancet_sub_wf.md ├── kfdrc_mutect2_sub_wf.md ├── kfdrc_strelka2_subworkflow.md ├── kfdrc_vardict_sub_wf.md └── somatic_annotation_wf.png ├── scripts ├── add_strelka2_fields.py ├── consensus_merge.py ├── hotspot.py ├── kf_mskcc_vcf2maf_1.6.21.pl ├── sbg_cveto_util.py ├── sbg_multicnv.py ├── sbg_multicnv_methods.py └── sbg_multicnv_visualisations.py ├── sub_workflows ├── kfdrc_cnvkit_sub_wf.cwl ├── kfdrc_controlfreec_sub_wf.cwl ├── kfdrc_gatk_cnv_somatic_pair_wf.cwl ├── kfdrc_lancet_sub_wf.cwl ├── kfdrc_manta_sub_wf.cwl ├── kfdrc_mutect2_filter_support_subwf.cwl ├── kfdrc_mutect2_sub_wf.cwl ├── kfdrc_run_theta2_sub_wf.cwl ├── kfdrc_strelka2_sub_wf.cwl ├── kfdrc_vardict_sub_wf.cwl └── prepare_regions.cwl ├── tools ├── aa_classifier.cwl ├── add_basename.cwl ├── amplicon_architect.cwl ├── annotsv.cwl ├── awk_chrlen_builder.cwl ├── awk_min_seg_length.cwl ├── bcbio_filter_vardict_somatic.cwl ├── bcbio_normalize_vcf.cwl ├── bcbio_variant_recall_ensemble.cwl ├── bcftools_annotate.cwl ├── bcftools_reheader_samples_index.cwl ├── bedtools_intersect.cwl ├── bundle_secondaryfiles.cwl ├── bwa_index.cwl ├── canvas_paired_wes.cwl ├── clt_pass_file.cwl ├── cns_to_aa_bed.cwl ├── cnvkit_access.cwl ├── cnvkit_batch.cwl ├── cnvkit_batch_only.cwl ├── cnvkit_call.cwl ├── cnvkit_export_theta2.cwl ├── cnvkit_import_theta2.cwl ├── cnvnator.cwl ├── consensus_merge.cwl ├── control-freec-11-6-sbg.cwl ├── control_freec_mini_pileup.cwl ├── expression_flatten_file_list.cwl ├── expression_flatten_list.cwl ├── expression_pickvalue_workaround.cwl ├── expression_run_aa_if_wgs.cwl ├── gatk_Mutect2.cwl ├── gatk_annotateintervals.cwl ├── gatk_bedtointervallist.cwl ├── gatk_calculatecontamination.cwl ├── gatk_callcopyratiosegments.cwl ├── gatk_collectalleliccounts.cwl ├── gatk_collectreadcounts.cwl ├── gatk_createreadcountpanelofnormals.cwl ├── gatk_denoisereadcounts.cwl ├── gatk_filter_germline_variant.cwl ├── gatk_filtermutectcalls.cwl ├── gatk_funcotatesegments.cwl ├── gatk_gatherpileupsummaries.cwl ├── gatk_getpileupsummaries.cwl ├── gatk_indexfeaturefile.cwl ├── gatk_intervallisttobed.cwl ├── gatk_intervallisttool.cwl ├── gatk_intervallisttools.cwl ├── gatk_learnorientationbias.cwl ├── gatk_mergemutectstats.cwl ├── gatk_mergevcfs.cwl ├── gatk_modelsegments.cwl ├── gatk_plotdenoisedcopyratios.cwl ├── gatk_plotmodeledsegments.cwl ├── gatk_preprocessintervals.cwl ├── gatk_selectvariants.cwl ├── gatk_sortvcf.cwl ├── lancet.cwl ├── lumpy-sv_germline.cwl ├── lumpy-sv_somatic.cwl ├── manta.cwl ├── mode_defaults.cwl ├── mode_list_selector.cwl ├── mode_selector.cwl ├── picard_createsequencedictionary.cwl ├── prep_mnp_variants.cwl ├── prepare_aa.cwl ├── preprocess_lancet_intervals.cwl ├── python_vardict_interval_split.cwl ├── runtime_validator.cwl ├── samtools_calmd.cwl ├── samtools_cram2bam.cwl ├── samtools_faidx.cwl ├── samtools_reheader_bam.cwl ├── sb_multicnv_1_0_0.cwl ├── sb_multicnv_prepare_files_for_scatter.cwl ├── sb_multicnv_rename_files.cwl ├── seurat.cwl ├── smoove_lumpy.cwl ├── snpEff_annotate.cwl ├── speedseq_sv_annotate.cwl ├── strelka2.cwl ├── tabix_index.cwl ├── tar.cwl ├── telomerehunter.cwl ├── theta2_purity.cwl ├── ubuntu_ratio2seg.cwl ├── ubuntu_rename_outputs.cwl ├── untar_gzip.cwl └── vardictjava.cwl └── workflow ├── kfdrc-somatic-variant-workflow.cwl ├── kfdrc_consensus_calling.cwl ├── kfdrc_gatk_create_cnv_pon_wf.cwl └── kfdrc_production_amplicon_architect.cwl 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