├── .gitignore ├── HCC2218-sv ├── HCC2218-sv-workflow │ ├── main-HCC2218-sv-samples.json │ ├── main-HCC2218-sv.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_sv.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── calculate_sv_bins.cwl │ │ ├── calculate_sv_coverage.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── detect_sv.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── normalize_sv_coverage.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_sv.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ ├── wf-svcall.cwl │ └── wf-variantcall.cwl ├── HCC2218-sv.yaml ├── bcbio_system.yaml ├── download_data.sh ├── run_cromwell.sh └── run_generate_cwl.sh ├── LICENSE.txt ├── NA12878-chr20 ├── NA12878-platinum-chr20-wdl │ ├── alignment.wdl │ ├── main_NA12878_platinum_chr20.wdl │ └── variantcall.wdl ├── NA12878-platinum-chr20-workflow-arvados │ ├── main-NA12878-platinum-chr20-samples.json │ ├── main-NA12878-platinum-chr20.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_grading_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── NA12878-platinum-chr20-workflow-s3 │ └── main-NA12878-platinum-chr20-samples.json ├── NA12878-platinum-chr20-workflow │ ├── main-NA12878-platinum-chr20-samples.json │ ├── main-NA12878-platinum-chr20.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── NA12878-platinum-chr20.csv ├── bcbio_system.yaml ├── bcbio_system_arvados.yaml ├── bcbio_system_s3.yaml ├── download_data.sh ├── ga4gh_execution_challenge │ ├── bcbio_NA12878-chr20_checker.json │ ├── bcbio_NA12878-chr20_submit.json │ ├── grading-summary-NA12878-chr20-baseline.csv │ ├── link_cwl.sh │ ├── link_to_synapse.py │ └── upload_biodata.sh ├── germline_template.yaml ├── run_bunny.sh ├── run_cwltool.sh ├── run_generate_cwl.sh ├── run_generate_cwl_arvados.sh ├── run_generate_cwl_s3.sh ├── run_generate_wdl.sh ├── run_toil.sh └── run_toil_aws.sh ├── NA24385-sv ├── NA24385-sv-workflow │ ├── main-NA24385-sv-samples.json │ ├── main-NA24385-sv.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_sv.cwl │ │ ├── calculate_sv_bins.cwl │ │ ├── calculate_sv_coverage.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── detect_sv.cwl │ │ ├── multiqc_summary.cwl │ │ ├── normalize_sv_coverage.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ └── summarize_sv.cwl │ ├── wf-alignment.cwl │ └── wf-svcall.cwl ├── NA24385-sv.yaml ├── bcbio_system.yaml ├── download_data.sh ├── run_bunny.sh ├── run_cromwell.sh ├── run_generate_cwl.sh └── run_toil.sh ├── README.md ├── SGDP-recall-CGC ├── SGDP-recall-cgc │ ├── main-SGDP-recall-samples.json │ ├── main-SGDP-recall.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_grading_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── SGDP-recall-standalone.cwl ├── SGDP-recall.csv ├── SGDP-recall │ └── config │ │ ├── SGDP-recall-template.yaml │ │ ├── SGDP-recall.csv │ │ └── SGDP-recall.yaml ├── bcbio_system_cgc.yaml ├── germline_template.yaml ├── run_generate_cwl_cgc.sh ├── run_upload_cgc.sh └── upload_to_cgc.py ├── giab-chm ├── README.md ├── bcbio_system-local.yaml ├── download_data.sh ├── germline-template.yaml ├── giab-chm-workflow │ ├── main-giab-chm-samples.json │ ├── main-giab-chm.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── giab-chm.csv ├── prep_chm_truth.py ├── prep_chm_truth.sh ├── run_bunny.sh └── run_generate_cwl.sh ├── giab-exome ├── bcbio_system-local.yaml ├── download_data.sh ├── germline-template.yaml ├── giab-exome-workflow │ ├── main-giab-exome-samples.json │ ├── main-giab-exome.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── giab-exome.csv ├── input │ └── get_data.sh ├── run_cromwell.sh └── run_generate_cwl.sh ├── giab-joint ├── arvados │ ├── bcbio_system-arvados.yaml │ ├── run_arvados.sh │ └── run_generate_cwl.sh ├── bcbio_system.yaml ├── dnanexus │ ├── bcbio_system-dnanexus.yaml │ ├── run_compile.sh │ ├── run_dnanexus.sh │ └── run_generate_cwl.sh ├── dnanexus_single │ ├── README.txt │ ├── bcbio_system-dnanexus.yaml │ ├── germline-template.yaml │ ├── giab-single-bwa.csv │ ├── giab-single-dragen.csv │ └── run_generate_cwl.sh ├── download_data.sh ├── ga4gh_execution_challenge │ ├── bcbio-giab-joint_checker.json │ ├── bcbio-giab-joint_submit.json │ ├── grading-summary-gj1-baseline.csv │ ├── link_cwl.sh │ ├── link_to_synapse.py │ └── upload_biodata.sh ├── giab-joint-workflow │ ├── main-giab-joint-samples.json │ ├── main-giab-joint.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_jointvc.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── concat_batch_variantcalls_jointvc.cwl │ │ ├── finalize_jointvc.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── get_parallel_regions_jointvc.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── run_jointvc.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ ├── wf-jointcall.cwl │ └── wf-variantcall.cwl ├── giab-joint.csv ├── joint-template.yaml ├── run_bunny.sh ├── run_generate_cwl.sh └── run_toil.sh ├── pgp ├── README.md ├── bcbio_system-arvados.yaml ├── pgp_sv_hla.yaml ├── run_arvados.sh ├── run_generate_cwl.sh └── scripts │ └── extract_veritas_pgp.py ├── somatic-giab-mix ├── bcbio_system.yaml ├── download_data.sh ├── run_bunny.sh ├── run_generate_cwl.sh ├── run_toil.sh ├── somatic-giab-mix-workflow │ ├── main-somatic-giab-mix-samples.json │ ├── main-somatic-giab-mix.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── somatic-giab-mix.csv └── somatic-template.yaml ├── somatic-lowfreq ├── bcbio_system.yaml ├── download_data.sh ├── pisces-ras-workflow │ ├── main-pisces-ras-samples.json │ ├── main-pisces-ras.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── pisces-ras.yaml ├── pisces-titr-workflow │ ├── main-pisces-titr-samples.json │ ├── main-pisces-titr.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl ├── pisces-titr.yaml ├── prepare_inputs │ ├── clean_truth_sets.py │ ├── prepare_bcbio_inputs.py │ ├── prepare_data.sh │ └── smcounter2 │ │ ├── convert_truth_vcf.py │ │ ├── fix_bam_umis.py │ │ └── prepare_data.sh ├── run_bunny.sh ├── run_cromwell.sh ├── run_generate_cwl.sh ├── smcounter2-umi-workflow │ ├── main-smcounter2-umi-samples.json │ ├── main-smcounter2-umi.cwl │ ├── steps │ │ ├── alignment_to_rec.cwl │ │ ├── batch_for_variantcall.cwl │ │ ├── combine_sample_regions.cwl │ │ ├── compare_to_rm.cwl │ │ ├── concat_batch_variantcalls.cwl │ │ ├── get_parallel_regions.cwl │ │ ├── merge_split_alignments.cwl │ │ ├── multiqc_summary.cwl │ │ ├── pipeline_summary.cwl │ │ ├── postprocess_alignment.cwl │ │ ├── postprocess_alignment_to_rec.cwl │ │ ├── postprocess_variants.cwl │ │ ├── prep_align_inputs.cwl │ │ ├── prep_samples.cwl │ │ ├── prep_samples_to_rec.cwl │ │ ├── process_alignment.cwl │ │ ├── qc_to_rec.cwl │ │ ├── summarize_vc.cwl │ │ └── variantcall_batch_region.cwl │ ├── wf-alignment.cwl │ └── wf-variantcall.cwl └── smcounter2-umi.yaml └── wes-agha-test ├── README.md ├── bcbio-validation-checker ├── Dockstore.cwl ├── checker-workflow-wrapper.json └── grading-summary-combined-expected.csv ├── bcbio_system-arvados.yaml ├── bcbio_system-gcp.yaml ├── checker-workflow-wrapping-tool.cwl ├── run_arvados.sh ├── run_cromwell.sh ├── run_generate_cwl_arvados.sh ├── run_generate_cwl_gcp.sh ├── wes_chr21_test-template.yaml ├── wes_chr21_test-workflow-arvados ├── main-wes_chr21_test-samples.json ├── main-wes_chr21_test.cwl ├── steps │ ├── alignment_to_rec.cwl │ ├── batch_for_ensemble.cwl │ ├── batch_for_sv.cwl │ ├── batch_for_variantcall.cwl │ ├── calculate_sv_bins.cwl │ ├── calculate_sv_coverage.cwl │ ├── combine_calls.cwl │ ├── combine_sample_regions.cwl │ ├── compare_to_rm.cwl │ ├── concat_batch_variantcalls.cwl │ ├── detect_sv.cwl │ ├── get_parallel_regions.cwl │ ├── merge_split_alignments.cwl │ ├── multiqc_summary.cwl │ ├── normalize_sv_coverage.cwl │ ├── pipeline_summary.cwl │ ├── postprocess_alignment.cwl │ ├── postprocess_alignment_to_rec.cwl │ ├── postprocess_variants.cwl │ ├── prep_align_inputs.cwl │ ├── prep_samples.cwl │ ├── prep_samples_to_rec.cwl │ ├── process_alignment.cwl │ ├── qc_to_rec.cwl │ ├── summarize_sv.cwl │ ├── summarize_vc.cwl │ └── variantcall_batch_region.cwl ├── wf-alignment.cwl ├── wf-svcall.cwl └── wf-variantcall.cwl ├── wes_chr21_test-workflow-gcp ├── main-wes_chr21_test-samples.json ├── main-wes_chr21_test.cwl ├── steps │ ├── alignment_to_rec.cwl │ ├── batch_for_ensemble.cwl │ ├── batch_for_sv.cwl │ ├── batch_for_variantcall.cwl │ ├── calculate_sv_bins.cwl │ ├── calculate_sv_coverage.cwl │ ├── combine_calls.cwl │ ├── combine_sample_regions.cwl │ ├── compare_to_rm.cwl │ ├── concat_batch_variantcalls.cwl │ ├── detect_sv.cwl │ ├── get_parallel_regions.cwl │ ├── merge_split_alignments.cwl │ ├── multiqc_summary.cwl │ ├── normalize_sv_coverage.cwl │ ├── pipeline_summary.cwl │ ├── postprocess_alignment.cwl │ ├── postprocess_alignment_to_rec.cwl │ ├── postprocess_variants.cwl │ ├── prep_align_inputs.cwl │ ├── prep_samples.cwl │ ├── prep_samples_to_rec.cwl │ ├── process_alignment.cwl │ ├── qc_to_rec.cwl │ ├── summarize_sv.cwl │ ├── summarize_vc.cwl │ └── variantcall_batch_region.cwl ├── wf-alignment.cwl ├── wf-svcall.cwl └── wf-variantcall.cwl └── wes_chr21_test.csv /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/.gitignore -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/main-HCC2218-sv-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/main-HCC2218-sv-samples.json -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/main-HCC2218-sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/main-HCC2218-sv.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/batch_for_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/batch_for_sv.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/calculate_sv_bins.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/calculate_sv_bins.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/calculate_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/calculate_sv_coverage.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/detect_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/detect_sv.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/normalize_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/normalize_sv_coverage.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/summarize_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/summarize_sv.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/wf-svcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/wf-svcall.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /HCC2218-sv/HCC2218-sv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/HCC2218-sv.yaml -------------------------------------------------------------------------------- /HCC2218-sv/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/bcbio_system.yaml -------------------------------------------------------------------------------- /HCC2218-sv/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/download_data.sh -------------------------------------------------------------------------------- /HCC2218-sv/run_cromwell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/run_cromwell.sh -------------------------------------------------------------------------------- /HCC2218-sv/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/HCC2218-sv/run_generate_cwl.sh -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-wdl/alignment.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-wdl/alignment.wdl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-wdl/main_NA12878_platinum_chr20.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-wdl/main_NA12878_platinum_chr20.wdl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-wdl/variantcall.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-wdl/variantcall.wdl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20-samples.json -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_samples.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/process_alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/summarize_grading_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/summarize_grading_vc.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/wf-alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/wf-variantcall.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow-s3/main-NA12878-platinum-chr20-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow-s3/main-NA12878-platinum-chr20-samples.json -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20-samples.json -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /NA12878-chr20/NA12878-platinum-chr20.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/NA12878-platinum-chr20.csv -------------------------------------------------------------------------------- /NA12878-chr20/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/bcbio_system.yaml -------------------------------------------------------------------------------- /NA12878-chr20/bcbio_system_arvados.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/bcbio_system_arvados.yaml -------------------------------------------------------------------------------- /NA12878-chr20/bcbio_system_s3.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/bcbio_system_s3.yaml -------------------------------------------------------------------------------- /NA12878-chr20/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/download_data.sh -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/bcbio_NA12878-chr20_checker.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/bcbio_NA12878-chr20_checker.json -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/bcbio_NA12878-chr20_submit.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/bcbio_NA12878-chr20_submit.json -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/grading-summary-NA12878-chr20-baseline.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/grading-summary-NA12878-chr20-baseline.csv -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/link_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/link_cwl.sh -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/link_to_synapse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/link_to_synapse.py -------------------------------------------------------------------------------- /NA12878-chr20/ga4gh_execution_challenge/upload_biodata.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/ga4gh_execution_challenge/upload_biodata.sh -------------------------------------------------------------------------------- /NA12878-chr20/germline_template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/germline_template.yaml -------------------------------------------------------------------------------- /NA12878-chr20/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_bunny.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_cwltool.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_cwltool.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_generate_cwl.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_generate_cwl_arvados.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_generate_cwl_arvados.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_generate_cwl_s3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_generate_cwl_s3.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_generate_wdl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_generate_wdl.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_toil.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_toil.sh -------------------------------------------------------------------------------- /NA12878-chr20/run_toil_aws.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA12878-chr20/run_toil_aws.sh -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/main-NA24385-sv-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv-samples.json -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/batch_for_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/batch_for_sv.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/calculate_sv_bins.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/calculate_sv_bins.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/calculate_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/calculate_sv_coverage.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/detect_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/detect_sv.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/normalize_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/normalize_sv_coverage.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/steps/summarize_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/steps/summarize_sv.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv-workflow/wf-svcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv-workflow/wf-svcall.cwl -------------------------------------------------------------------------------- /NA24385-sv/NA24385-sv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/NA24385-sv.yaml -------------------------------------------------------------------------------- /NA24385-sv/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/bcbio_system.yaml -------------------------------------------------------------------------------- /NA24385-sv/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/download_data.sh -------------------------------------------------------------------------------- /NA24385-sv/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/run_bunny.sh -------------------------------------------------------------------------------- /NA24385-sv/run_cromwell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/run_cromwell.sh -------------------------------------------------------------------------------- /NA24385-sv/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/run_generate_cwl.sh -------------------------------------------------------------------------------- /NA24385-sv/run_toil.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/NA24385-sv/run_toil.sh -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/README.md -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall-samples.json -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/process_alignment.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/summarize_grading_vc.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-cgc/wf-variantcall.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall-standalone.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall-standalone.cwl -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall.csv: -------------------------------------------------------------------------------- 1 | samplename,description,sex 2 | LP6005443-DNA_H08.srt.aln.bam,S_Dinka-1,male 3 | -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall/config/SGDP-recall-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall/config/SGDP-recall-template.yaml -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall/config/SGDP-recall.csv: -------------------------------------------------------------------------------- 1 | samplename,description,sex 2 | LP6005443-DNA_H08.srt.aln.bam,S_Dinka-1,male 3 | -------------------------------------------------------------------------------- /SGDP-recall-CGC/SGDP-recall/config/SGDP-recall.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/SGDP-recall/config/SGDP-recall.yaml -------------------------------------------------------------------------------- /SGDP-recall-CGC/bcbio_system_cgc.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/bcbio_system_cgc.yaml -------------------------------------------------------------------------------- /SGDP-recall-CGC/germline_template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/germline_template.yaml -------------------------------------------------------------------------------- /SGDP-recall-CGC/run_generate_cwl_cgc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/run_generate_cwl_cgc.sh -------------------------------------------------------------------------------- /SGDP-recall-CGC/run_upload_cgc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/run_upload_cgc.sh -------------------------------------------------------------------------------- /SGDP-recall-CGC/upload_to_cgc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/SGDP-recall-CGC/upload_to_cgc.py -------------------------------------------------------------------------------- /giab-chm/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/README.md -------------------------------------------------------------------------------- /giab-chm/bcbio_system-local.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/bcbio_system-local.yaml -------------------------------------------------------------------------------- /giab-chm/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/download_data.sh -------------------------------------------------------------------------------- /giab-chm/germline-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/germline-template.yaml -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/main-giab-chm-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/main-giab-chm-samples.json -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/main-giab-chm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/main-giab-chm.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /giab-chm/giab-chm.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/giab-chm.csv -------------------------------------------------------------------------------- /giab-chm/prep_chm_truth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/prep_chm_truth.py -------------------------------------------------------------------------------- /giab-chm/prep_chm_truth.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/prep_chm_truth.sh -------------------------------------------------------------------------------- /giab-chm/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/run_bunny.sh -------------------------------------------------------------------------------- /giab-chm/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-chm/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-exome/bcbio_system-local.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/bcbio_system-local.yaml -------------------------------------------------------------------------------- /giab-exome/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/download_data.sh -------------------------------------------------------------------------------- /giab-exome/germline-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/germline-template.yaml -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/main-giab-exome-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/main-giab-exome-samples.json -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/main-giab-exome.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/main-giab-exome.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /giab-exome/giab-exome.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/giab-exome.csv -------------------------------------------------------------------------------- /giab-exome/input/get_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/input/get_data.sh -------------------------------------------------------------------------------- /giab-exome/run_cromwell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/run_cromwell.sh -------------------------------------------------------------------------------- /giab-exome/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-exome/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-joint/arvados/bcbio_system-arvados.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/arvados/bcbio_system-arvados.yaml -------------------------------------------------------------------------------- /giab-joint/arvados/run_arvados.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/arvados/run_arvados.sh -------------------------------------------------------------------------------- /giab-joint/arvados/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/arvados/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-joint/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/bcbio_system.yaml -------------------------------------------------------------------------------- /giab-joint/dnanexus/bcbio_system-dnanexus.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus/bcbio_system-dnanexus.yaml -------------------------------------------------------------------------------- /giab-joint/dnanexus/run_compile.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus/run_compile.sh -------------------------------------------------------------------------------- /giab-joint/dnanexus/run_dnanexus.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus/run_dnanexus.sh -------------------------------------------------------------------------------- /giab-joint/dnanexus/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/README.txt -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/bcbio_system-dnanexus.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/bcbio_system-dnanexus.yaml -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/germline-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/germline-template.yaml -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/giab-single-bwa.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/giab-single-bwa.csv -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/giab-single-dragen.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/giab-single-dragen.csv -------------------------------------------------------------------------------- /giab-joint/dnanexus_single/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/dnanexus_single/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-joint/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/download_data.sh -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/bcbio-giab-joint_checker.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/ga4gh_execution_challenge/bcbio-giab-joint_checker.json -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/bcbio-giab-joint_submit.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/ga4gh_execution_challenge/bcbio-giab-joint_submit.json -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/grading-summary-gj1-baseline.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/ga4gh_execution_challenge/grading-summary-gj1-baseline.csv -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/link_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/ga4gh_execution_challenge/link_cwl.sh -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/link_to_synapse.py: -------------------------------------------------------------------------------- 1 | ../../NA12878-chr20/ga4gh_execution_challenge/link_to_synapse.py -------------------------------------------------------------------------------- /giab-joint/ga4gh_execution_challenge/upload_biodata.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/ga4gh_execution_challenge/upload_biodata.sh -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/main-giab-joint-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/main-giab-joint-samples.json -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/main-giab-joint.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/main-giab-joint.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/batch_for_jointvc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/batch_for_jointvc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/finalize_jointvc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/finalize_jointvc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/get_parallel_regions_jointvc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/get_parallel_regions_jointvc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/run_jointvc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/run_jointvc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/wf-jointcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/wf-jointcall.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /giab-joint/giab-joint.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/giab-joint.csv -------------------------------------------------------------------------------- /giab-joint/joint-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/joint-template.yaml -------------------------------------------------------------------------------- /giab-joint/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/run_bunny.sh -------------------------------------------------------------------------------- /giab-joint/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/run_generate_cwl.sh -------------------------------------------------------------------------------- /giab-joint/run_toil.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/giab-joint/run_toil.sh -------------------------------------------------------------------------------- /pgp/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/README.md -------------------------------------------------------------------------------- /pgp/bcbio_system-arvados.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/bcbio_system-arvados.yaml -------------------------------------------------------------------------------- /pgp/pgp_sv_hla.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/pgp_sv_hla.yaml -------------------------------------------------------------------------------- /pgp/run_arvados.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/run_arvados.sh -------------------------------------------------------------------------------- /pgp/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/run_generate_cwl.sh -------------------------------------------------------------------------------- /pgp/scripts/extract_veritas_pgp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/pgp/scripts/extract_veritas_pgp.py -------------------------------------------------------------------------------- /somatic-giab-mix/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/bcbio_system.yaml -------------------------------------------------------------------------------- /somatic-giab-mix/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/download_data.sh -------------------------------------------------------------------------------- /somatic-giab-mix/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/run_bunny.sh -------------------------------------------------------------------------------- /somatic-giab-mix/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/run_generate_cwl.sh -------------------------------------------------------------------------------- /somatic-giab-mix/run_toil.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/run_toil.sh -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix-samples.json -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-giab-mix.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-giab-mix.csv -------------------------------------------------------------------------------- /somatic-giab-mix/somatic-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-giab-mix/somatic-template.yaml -------------------------------------------------------------------------------- /somatic-lowfreq/bcbio_system.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/bcbio_system.yaml -------------------------------------------------------------------------------- /somatic-lowfreq/download_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/download_data.sh -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/main-pisces-ras-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/main-pisces-ras-samples.json -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/main-pisces-ras.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/main-pisces-ras.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-ras.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-ras.yaml -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/main-pisces-titr-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/main-pisces-titr-samples.json -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/main-pisces-titr.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/main-pisces-titr.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/pisces-titr.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/pisces-titr.yaml -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/clean_truth_sets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/clean_truth_sets.py -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/prepare_bcbio_inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/prepare_bcbio_inputs.py -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/prepare_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/prepare_data.sh -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/smcounter2/convert_truth_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/smcounter2/convert_truth_vcf.py -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/smcounter2/fix_bam_umis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/smcounter2/fix_bam_umis.py -------------------------------------------------------------------------------- /somatic-lowfreq/prepare_inputs/smcounter2/prepare_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/prepare_inputs/smcounter2/prepare_data.sh -------------------------------------------------------------------------------- /somatic-lowfreq/run_bunny.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/run_bunny.sh -------------------------------------------------------------------------------- /somatic-lowfreq/run_cromwell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/run_cromwell.sh -------------------------------------------------------------------------------- /somatic-lowfreq/run_generate_cwl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/run_generate_cwl.sh -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/main-smcounter2-umi-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/main-smcounter2-umi-samples.json -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/main-smcounter2-umi.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/main-smcounter2-umi.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/prep_samples.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/process_alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/wf-alignment.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi-workflow/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi-workflow/wf-variantcall.cwl -------------------------------------------------------------------------------- /somatic-lowfreq/smcounter2-umi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/somatic-lowfreq/smcounter2-umi.yaml -------------------------------------------------------------------------------- /wes-agha-test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/README.md -------------------------------------------------------------------------------- /wes-agha-test/bcbio-validation-checker/Dockstore.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/bcbio-validation-checker/Dockstore.cwl -------------------------------------------------------------------------------- /wes-agha-test/bcbio-validation-checker/checker-workflow-wrapper.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/bcbio-validation-checker/checker-workflow-wrapper.json -------------------------------------------------------------------------------- /wes-agha-test/bcbio-validation-checker/grading-summary-combined-expected.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/bcbio-validation-checker/grading-summary-combined-expected.csv -------------------------------------------------------------------------------- /wes-agha-test/bcbio_system-arvados.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/bcbio_system-arvados.yaml -------------------------------------------------------------------------------- /wes-agha-test/bcbio_system-gcp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/bcbio_system-gcp.yaml -------------------------------------------------------------------------------- /wes-agha-test/checker-workflow-wrapping-tool.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/checker-workflow-wrapping-tool.cwl -------------------------------------------------------------------------------- /wes-agha-test/run_arvados.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/run_arvados.sh -------------------------------------------------------------------------------- /wes-agha-test/run_cromwell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/run_cromwell.sh -------------------------------------------------------------------------------- /wes-agha-test/run_generate_cwl_arvados.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/run_generate_cwl_arvados.sh -------------------------------------------------------------------------------- /wes-agha-test/run_generate_cwl_gcp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/run_generate_cwl_gcp.sh -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-template.yaml -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/main-wes_chr21_test-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/main-wes_chr21_test-samples.json -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/main-wes_chr21_test.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/main-wes_chr21_test.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_ensemble.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_ensemble.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/calculate_sv_bins.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/calculate_sv_bins.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/calculate_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/calculate_sv_coverage.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/combine_calls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/combine_calls.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/detect_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/detect_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/normalize_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/normalize_sv_coverage.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_samples.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/process_alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/summarize_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/summarize_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/wf-alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/wf-svcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/wf-svcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-arvados/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-arvados/wf-variantcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/wf-alignment.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/wf-alignment.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/wf-svcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/wf-svcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test-workflow-gcp/wf-variantcall.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test-workflow-gcp/wf-variantcall.cwl -------------------------------------------------------------------------------- /wes-agha-test/wes_chr21_test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcbio/bcbio_validation_workflows/HEAD/wes-agha-test/wes_chr21_test.csv --------------------------------------------------------------------------------