{"@id":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"509938802c5e42bb8084c6a5a26ab6425c60e69a","path":"definitions/pipelines/somatic_exome_cle.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","url":"https://github.com/genome/analysis-workflows/blob/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl"},"retrievedOn":"2026-10-22T05:39:32.473+00:00","lastCommit":"509938802c5e42bb8084c6a5a26ab6425c60e69a","label":"exome alignment and somatic variant detection for cle purpose","inputs":{"docm_vcf":{"type":"File"},"omni_vcf":{"type":"File"},"vep_pick":{},"reference":{"type":"String"},"tumor_name":{"type":"String (Optional)"},"normal_name":{"type":"String (Optional)"},"somalier_vcf":{"type":"File"},"scatter_count":{"doc":"scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs","type":"Integer"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"Directory"},"bait_intervals":{"type":"File"},"bqsr_intervals":{"type":"String[]"},"cle_vcf_filter":{"type":"Boolean"},"tumor_sequence":{"type":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/types/sequence_data.yml#sequence_data[]"},"disclaimer_text":{"type":"String (Optional)"},"normal_sequence":{"type":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/types/sequence_data.yml#sequence_data[]"},"varscan_p_value":{"type":"Float (Optional)"},"bqsr_known_sites":{"doc":"One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.","type":"File[]"},"target_intervals":{"label":"target_intervals: interval_list file of targets used in the sequencing experiment","doc":"target_intervals is an interval_list corresponding to the targets for the capture reagent.\nBED files with this information can be converted to interval_lists with Picard BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n","type":"File"},"summary_intervals":{"type":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/types/labelled_file.yml#labelled_file[]"},"tumor_sample_name":{"type":"String"},"disclaimer_version":{"type":"String"},"normal_sample_name":{"type":"String"},"per_base_intervals":{"type":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/types/labelled_file.yml#labelled_file[]"},"pindel_insert_size":{"type":"Integer"},"vep_ensembl_species":{"doc":"ensembl species - Must be present in the cache directory. 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file\"];\n  \"annotated_filter_vcf_index\" [label=\"vcf index\"];\n  \"tumor_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"normal_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"pad_target_intervals\" [label=\"expand interval list regions by a given number of basepairs\"];\n  \"tumor_index_cram\" [label=\"samtools index cram\"];\n  \"add_disclaimer_to_final_filtered_vcf\" [label=\"Insert an arbitrary string at a specific line of a gzipped file\"];\n  \"somalier_vcf\" -> \"concordance\" [label=\"vcf\"];\n  \"reference\" -> \"concordance\" [label=\"reference\"];\n  \"normal_alignment_and_qc\" -> \"concordance\" [label=\"bam_2\"];\n  \"tumor_alignment_and_qc\" -> \"concordance\" [label=\"bam_1\"];\n  \"detect_variants\" -> \"add_disclaimer_to_final_tsv\" [label=\"input_file\"];\n  \"default1\" -> \"add_disclaimer_to_final_tsv\" [label=\"line_number\"];\n  \"default1\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_final_tsv\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_to_final_tsv\" [label=\"output_name\"];\n  \"bait_intervals\" -> \"normal_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"normal_name\" -> \"normal_alignment_and_qc\" [label=\"final_name\"];\n  \"normal_sequence\" -> \"normal_alignment_and_qc\" [label=\"sequence\"];\n  \"bqsr_known_sites\" -> \"normal_alignment_and_qc\" [label=\"bqsr_known_sites\"];\n  \"omni_vcf\" -> \"normal_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"qc_minimum_base_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"target_intervals\" -> \"normal_alignment_and_qc\" [label=\"target_intervals\"];\n  \"summary_intervals\" -> \"normal_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"reference\" -> \"normal_alignment_and_qc\" [label=\"reference\"];\n  \"per_target_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"per_base_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"picard_metric_accumulation_level\" -> \"normal_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bqsr_intervals\" -> \"normal_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"normal_bam_to_cram\" -> \"normal_index_cram\" [label=\"cram\"];\n  \"varscan_max_normal_freq\" -> \"detect_variants\" [label=\"varscan_max_normal_freq\"];\n  \"tumor_alignment_and_qc\" -> \"detect_variants\" [label=\"tumor_bam\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"docm_vcf\" -> \"detect_variants\" [label=\"docm_vcf\"];\n  \"default2\" -> \"detect_variants\" [label=\"strelka_exome_mode\"];\n  \"default2\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"varscan_min_var_freq\" -> \"detect_variants\" [label=\"varscan_min_var_freq\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"varscan_strand_filter\" -> \"detect_variants\" [label=\"varscan_strand_filter\"];\n  \"strelka_cpu_reserved\" -> \"detect_variants\" [label=\"strelka_cpu_reserved\"];\n  \"cle_vcf_filter\" -> \"detect_variants\" [label=\"cle_vcf_filter\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"filter_docm_variants\" -> \"detect_variants\" [label=\"filter_docm_variants\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"pad_target_intervals\" -> \"detect_variants\" [label=\"roi_intervals\"];\n  \"pindel_insert_size\" -> \"detect_variants\" [label=\"pindel_insert_size\"];\n  \"filter_somatic_llr_normal_contamination_rate\" -> \"detect_variants\" [label=\"filter_somatic_llr_normal_contamination_rate\"];\n  \"filter_somatic_llr_tumor_purity\" -> \"detect_variants\" [label=\"filter_somatic_llr_tumor_purity\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"vep_pick\" -> \"detect_variants\" [label=\"vep_pick\"];\n  \"scatter_count\" -> \"detect_variants\" [label=\"scatter_count\"];\n  \"varscan_min_coverage\" -> \"detect_variants\" [label=\"varscan_min_coverage\"];\n  \"filter_somatic_llr_threshold\" -> \"detect_variants\" [label=\"filter_somatic_llr_threshold\"];\n  \"filter_minimum_depth\" -> \"detect_variants\" [label=\"filter_minimum_depth\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"tumor_sample_name\" -> \"detect_variants\" [label=\"tumor_sample_name\"];\n  \"normal_alignment_and_qc\" -> \"detect_variants\" [label=\"normal_bam\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"vep_custom_annotations\" -> \"detect_variants\" [label=\"vep_custom_annotations\"];\n  \"normal_sample_name\" -> \"detect_variants\" [label=\"normal_sample_name\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"varscan_p_value\" -> \"detect_variants\" [label=\"varscan_p_value\"];\n  \"per_target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"omni_vcf\" -> \"tumor_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"target_intervals\"];\n  \"tumor_name\" -> \"tumor_alignment_and_qc\" [label=\"final_name\"];\n  \"bqsr_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"qc_minimum_base_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"tumor_sequence\" -> \"tumor_alignment_and_qc\" [label=\"sequence\"];\n  \"summary_intervals\" -> \"tumor_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"reference\" -> \"tumor_alignment_and_qc\" [label=\"reference\"];\n  \"bait_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"per_base_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"bqsr_known_sites\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_known_sites\"];\n  \"picard_metric_accumulation_level\" -> \"tumor_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"add_disclaimer_to_final_tsv\" -> \"add_disclaimer_version_to_final_tsv\" [label=\"input_file\"];\n  \"add_disclaimer_to_final_tsv\" -> \"add_disclaimer_version_to_final_tsv\" [label=\"output_name\"];\n  \"disclaimer_version\" -> \"add_disclaimer_version_to_final_tsv\" [label=\"some_text\"];\n  \"default3\" -> \"add_disclaimer_version_to_final_tsv\" [label=\"line_number\"];\n  \"default3\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"add_disclaimer_to_final_filtered_vcf\" -> \"add_disclaimer_version_to_final_filtered_vcf\" [label=\"output_name\"];\n  \"default4\" -> \"add_disclaimer_version_to_final_filtered_vcf\" [label=\"line_number\"];\n  \"default4\" [label=\"3\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_version\" -> \"add_disclaimer_version_to_final_filtered_vcf\" [label=\"some_text\"];\n  \"add_disclaimer_to_final_filtered_vcf\" -> \"add_disclaimer_version_to_final_filtered_vcf\" [label=\"input_file\"];\n  \"add_disclaimer_version_to_final_filtered_vcf\" -> \"annotated_filter_vcf_index\" [label=\"vcf\"];\n  \"reference\" -> \"tumor_bam_to_cram\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_bam_to_cram\" [label=\"bam\"];\n  \"normal_alignment_and_qc\" -> \"normal_bam_to_cram\" [label=\"bam\"];\n  \"reference\" -> \"normal_bam_to_cram\" [label=\"reference\"];\n  \"target_interval_padding\" -> \"pad_target_intervals\" [label=\"roi_padding\"];\n  \"target_intervals\" -> \"pad_target_intervals\" [label=\"interval_list\"];\n  \"tumor_bam_to_cram\" -> \"tumor_index_cram\" [label=\"cram\"];\n  \"detect_variants\" -> \"add_disclaimer_to_final_filtered_vcf\" [label=\"input_file\"];\n  \"detect_variants\" -> \"add_disclaimer_to_final_filtered_vcf\" [label=\"output_name\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_final_filtered_vcf\" [label=\"some_text\"];\n  \"default5\" -> \"add_disclaimer_to_final_filtered_vcf\" [label=\"line_number\"];\n  \"default5\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_flagstats\";\n  \"detect_variants\" -> \"varscan_unfiltered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_mark_duplicates_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_summary_hs_metrics\";\n  \"concordance\" -> \"somalier_concordance_metrics\";\n  \"tumor_index_cram\" -> \"tumor_cram\";\n  \"detect_variants\" -> \"strelka_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_depth\";\n  \"concordance\" -> \"somalier_concordance_statistics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_coverage_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_alignment_summary_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_coverage_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_insert_size_metrics\";\n  \"normal_index_cram\" -> \"normal_cram\";\n  \"detect_variants\" -> \"varscan_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_hs_metrics\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"detect_variants\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_coverage_metrics\";\n  \"detect_variants\" -> \"pindel_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_hs_metrics\";\n  \"detect_variants\" -> \"mutect_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_hs_metrics\";\n  \"detect_variants\" -> \"docm_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_hs_metrics\";\n  \"detect_variants\" -> \"strelka_unfiltered_vcf\";\n  \"detect_variants\" -> \"normal_indel_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_coverage_metrics\";\n  \"detect_variants\" -> \"normal_snv_bam_readcount_tsv\";\n  \"detect_variants\" -> \"pindel_unfiltered_vcf\";\n  \"annotated_filter_vcf_index\" -> \"final_filtered_vcf\";\n  \"add_disclaimer_version_to_final_tsv\" -> \"final_tsv\";\n  \"tumor_alignment_and_qc\" -> \"tumor_alignment_summary_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_depth\";\n  \"normal_alignment_and_qc\" -> \"normal_summary_hs_metrics\";\n  \"detect_variants\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_hs_metrics\";\n  \"detect_variants\" -> \"mutect_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_insert_size_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_flagstats\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"tumor_alignment_and_qc\" -> \"tumor_mark_duplicates_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/pipelines/somatic_exome_cle.cwl","licenseName":"MIT License"}