-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #50 from eastgenomics/DI-623_3.0.0
DI-623 3.0.0 (#50)
- Loading branch information
Showing
2 changed files
with
224 additions
and
14 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,192 @@ | ||
| { | ||
| "assay": "CEN", | ||
| "version": "3.0.0", | ||
| "cnv_call_app_id": "app-GZ4pXxj4xG062Bj5zjgP1Bb0", | ||
| "artemis_app_id": "app-GZ1X5zj4K5ZxyfYPPq4YgGv3", | ||
| "snv_report_workflow_id": "workflow-GXzkfYj4QPQp9z4Jz4BF09y6", | ||
| "cnv_report_workflow_id": "workflow-GXzvJq84XZB1fJk9fBfG88XJ", | ||
| "reference_files": { | ||
| "genepanels": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GVx0vkQ433Gvq63k1Kj4Y562", | ||
| "exons_nirvana": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF611Z8433Gk7gZ47gypK7ZZ", | ||
| "genes2transcripts": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GV4P970433Gj6812zGVBZvB4", | ||
| "exonsfile": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF611Z8433Gf99pBPbJkV7bq" | ||
| }, | ||
| "name_patterns": { | ||
| "Epic": "^[\\d\\w]+-[\\d\\w]+", | ||
| "Gemini": "^X[\\d]+" | ||
| }, | ||
| "modes": { | ||
| "cnv_call": { | ||
| "instance_type": "mem2_ssd1_v2_x16", | ||
| "inputs": { | ||
| "bambais": { | ||
| "folder": "/sentieon-dnaseq/", | ||
| "name": ".bam$|.bam.bai$" | ||
| }, | ||
| "GATK_docker": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GBBP9JQ433GxV97xBpQkzYZx" | ||
| } | ||
| }, | ||
| "annotation_tsv": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GFPxzPQ4V50z4pv230p82G0q" | ||
| } | ||
| }, | ||
| "interval_list": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GFPxzKj4V50pJX3F4vV58yyg" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "cnv_reports": { | ||
| "stage_instance_types": { | ||
| }, | ||
| "inputs": { | ||
| "stage-cnv_generate_bed_vep.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-cnv_generate_bed_vep.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-cnv_generate_bed_vep.gene_panels": "INPUT-genepanels", | ||
| "stage-cnv_generate_bed_vep.flank": 495, | ||
| "stage-cnv_generate_bed_vep.additional_regions": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GJZQvg0433GkyFZg13K6VV6p" | ||
| } | ||
| }, | ||
| "stage-cnv_vep.config_file": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GQGJ3Z84xyx0jp1q65K1Q1jY" | ||
| } | ||
| }, | ||
| "stage-cnv_vep.vcf": { | ||
| "folder": "CNV_vcfs", | ||
| "name": "_segments.vcf$" | ||
| }, | ||
| "stage-cnv_generate_bed_excluded.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-cnv_generate_bed_excluded.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-cnv_generate_bed_excluded.gene_panels": "INPUT-genepanels", | ||
| "stage-cnv_generate_bed_excluded.additional_regions": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GJZQvg0433GkyFZg13K6VV6p" | ||
| } | ||
| }, | ||
| "stage-cnv_generate_bed_excluded.flank": 0, | ||
| "stage-cnv_annotate_excluded_regions.cds_hgnc": "INPUT-exons_nirvana", | ||
| "stage-cnv_annotate_excluded_regions.cds_gene": "INPUT-exonsfile", | ||
| "stage-cnv_annotate_excluded_regions.additional_regions": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GJZQvg0433GkyFZg13K6VV6p" | ||
| } | ||
| }, | ||
| "stage-cnv_annotate_excluded_regions.excluded_regions": { | ||
| "folder": "CNV_summary", | ||
| "name": "_excluded_intervals.bed$" | ||
| }, | ||
| "stage-cnv_generate_workbook.additional_sheet_names": "ExcludedRegions", | ||
| "stage-cnv_generate_workbook.exclude_columns": "REF FILTER CSQ_Allele CSQ_Consequence CSQ_IMPACT", | ||
| "stage-cnv_generate_workbook.acmg": true, | ||
| "stage-cnv_generate_workbook.reorder_columns": "CHROM POS END CNVLEN ID ALT QUAL CSQ_SYMBOL CSQ_Feature CSQ_VARIANT_CLASS CSQ_EXON CSQ_INTRON CSQ_STRAND GT CN NP QA QS QSE QSS", | ||
| "stage-cnv_generate_workbook.add_comment_column": true, | ||
| "stage-cnv_generate_workbook.summary": "dias" | ||
| } | ||
| }, | ||
| "snv_reports": { | ||
| "stage_instance_types": { | ||
| }, | ||
| "inputs": { | ||
| "stage-rpt_generate_bed_athena.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-rpt_generate_bed_athena.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-rpt_generate_bed_athena.gene_panels": "INPUT-genepanels", | ||
| "stage-rpt_generate_bed_vep.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-rpt_generate_bed_vep.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-rpt_generate_bed_vep.gene_panels": "INPUT-genepanels", | ||
| "stage-rpt_generate_bed_vep.flank": 495, | ||
| "stage-rpt_vep.config_file": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GbPYpkQ4z6jBQxkqYBF32821" | ||
| } | ||
| }, | ||
| "stage-rpt_vep.vcf": { | ||
| "folder": "sentieon-dnaseq", | ||
| "name": "^[^\\.]*(?!\\.g)\\.vcf(\\.gz)?$" | ||
| }, | ||
| "stage-rpt_generate_workbook.exclude_columns": "BaseQRankSum ClippingRankSum DB ExcessHet FS MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR PL QUAL ID FILTER CSQ_ClinVar_CLNSIGCONF CSQ_Allele CSQ_HGNC_ID DP AC AF AN CSQ_SpliceAI_pred_DP_AL CSQ_SpliceAI_pred_DP_AG CSQ_SpliceAI_pred_DP_DG CSQ_SpliceAI_pred_DP_DL CSQ_gnomADe_AC_popmax CSQ_gnomADe_AF_popmax CSQ_gnomADe_AN_popmax CSQ_gnomADe_nhomalt_popmax CSQ_gnomADe_non_cancer_AC CSQ_gnomADe_non_cancer_AC_popmax CSQ_gnomADe_non_cancer_AF CSQ_gnomADe_non_cancer_AF_popmax CSQ_gnomADe_non_cancer_AN CSQ_gnomADe_non_cancer_AN_popmax CSQ_gnomADe_non_cancer_nhomalt CSQ_gnomADe_non_cancer_nhomalt_popmax CSQ_gnomADe_non_cancer_popmax CSQ_gnomADe_popmax CSQ_gnomADg_AC_popmax CSQ_gnomADg_AF_popmax CSQ_gnomADg_AN_popmax CSQ_gnomADg_nhomalt_popmax CSQ_gnomADg_popmax", | ||
| "stage-rpt_generate_workbook.acmg": true, | ||
| "stage-rpt_generate_workbook.rename_columns": "CSQ_Feature=Transcript DP_FMT=DP", | ||
| "stage-rpt_generate_workbook.add_comment_column": true, | ||
| "stage-rpt_generate_workbook.keep_tmp": true, | ||
| "stage-rpt_generate_workbook.summary": "dias", | ||
| "stage-rpt_generate_workbook.filter": "bcftools filter -e '(CSQ_Consequence==\"synonymous_variant\" | CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"upstream_gene_variant\" | CSQ_Consequence==\"downstream_gene_variant\" | CSQ_Consequence==\"intergenic_variant\" | CSQ_Consequence==\"5_prime_UTR_variant\" | CSQ_Consequence==\"3_prime_UTR_variant\" | CSQ_gnomADe_AF>0.01 | CSQ_gnomADg_AF>0.01 | CSQ_TWE_AF>0.05) & CSQ_HGMD_CLASS!~ \"DM\" & CSQ_ClinVar_CLNSIG!~ \"pathogenic\\/i\" & CSQ_ClinVar_CLNSIGCONF!~ \"pathogenic\\/i\"'", | ||
| "stage-rpt_generate_workbook.human_filter": "excluded gnomAD exomes / genomes > 1%, TWE > 5%, synonymous / intronic / intergenic / upstream / downstream / UTRs EXCEPT pathogenic status in ClinVar OR DM in HGMD Class", | ||
| "stage-rpt_generate_workbook.reorder_columns": "CHROM POS REF ALT GT GQ DP_FMT AD CSQ_SYMBOL CSQ_EXON CSQ_INTRON CSQ_HGVSc CSQ_HGVSp CSQ_Consequence CSQ_IMPACT CSQ_VARIANT_CLASS CSQ_gnomADe_AF CSQ_gnomADe_Hom CSQ_gnomADe_AC CSQ_gnomADe_AN CSQ_gnomADe_nhomalt CSQ_gnomADg_AF CSQ_gnomADg_AC CSQ_gnomADg_AN CSQ_gnomADg_nhomalt CSQ_TWE_AF CSQ_TWE_AC_Hom CSQ_TWE_AC_Het CSQ_TWE_AN CSQ_HGMD CSQ_HGMD_CLASS CSQ_HGMD_RANKSCORE CSQ_HGMD_PHEN CSQ_Existing_variation CSQ_ClinVar CSQ_ClinVar_CLNDN CSQ_ClinVar_CLNSIG CSQ_Mastermind_MMID3 CSQ_CADD_PHRED CSQ_REVEL CSQ_SpliceAI_pred_DS_AG CSQ_SpliceAI_pred_DS_AL CSQ_SpliceAI_pred_DS_DG CSQ_SpliceAI_pred_DS_DL CSQ_HGVS_OFFSET CSQ_STRAND CSQ_Feature", | ||
| "stage-rpt_generate_workbook.freeze_column": "N2", | ||
| "stage-rpt_athena.exons_file": "INPUT-exonsfile", | ||
| "stage-rpt_athena.limit": 260, | ||
| "stage-rpt_athena.summary": true, | ||
| "stage-rpt_athena.mosdepth_files": { | ||
| "folder": "eggd_mosdepth", | ||
| "name": "per-base.bed.gz$|reference_build.txt$" | ||
| } | ||
| } | ||
| }, | ||
| "mosaic_reports": { | ||
| "stage_instance_types": { | ||
| }, | ||
| "inputs": { | ||
| "stage-rpt_generate_bed_athena.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-rpt_generate_bed_athena.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-rpt_generate_bed_athena.gene_panels": "INPUT-genepanels", | ||
| "stage-rpt_generate_bed_vep.exons_nirvana": "INPUT-exons_nirvana", | ||
| "stage-rpt_generate_bed_vep.nirvana_genes2transcripts": "INPUT-genes2transcripts", | ||
| "stage-rpt_generate_bed_vep.gene_panels": "INPUT-genepanels", | ||
| "stage-rpt_vep.config_file": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GbPYpkQ4z6jBQxkqYBF32821" | ||
| } | ||
| }, | ||
| "stage-rpt_vep.vcf": { | ||
| "folder": "tnhaplotyper", | ||
| "name": "^[^\\.]*(?!\\.g)\\.vcf(\\.gz)?$" | ||
| }, | ||
| "stage-rpt_generate_workbook.exclude_columns": "BaseQRankSum ClippingRankSum DB ExcessHet FS MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR PL QUAL ID FILTER CSQ_ClinVar_CLNSIGCONF CSQ_Allele CSQ_HGNC_ID DP AC AF AN CSQ_SpliceAI_pred_DP_AL CSQ_SpliceAI_pred_DP_AG CSQ_SpliceAI_pred_DP_DG CSQ_SpliceAI_pred_DP_DL AS_FilterStatus AS_SB_TABLE ECNT GERMQ MBQ MFRL MMQ MPOS POPAF ROQ TLOD F1R2 F2R1 SB CSQ_gnomADe_AC_popmax CSQ_gnomADe_AF_popmax CSQ_gnomADe_AN_popmax CSQ_gnomADe_nhomalt CSQ_gnomADe_nhomalt_popmax CSQ_gnomADe_non_cancer_AC CSQ_gnomADe_non_cancer_AC_popmax CSQ_gnomADe_non_cancer_AF CSQ_gnomADe_non_cancer_AF_popmax CSQ_gnomADe_non_cancer_AN CSQ_gnomADe_non_cancer_AN_popmax CSQ_gnomADe_non_cancer_nhomalt CSQ_gnomADe_non_cancer_nhomalt_popmax CSQ_gnomADe_non_cancer_popmax CSQ_gnomADe_popmax CSQ_gnomADg_AC_popmax CSQ_gnomADg_AF_popmax CSQ_gnomADg_AN_popmax CSQ_gnomADg_nhomalt CSQ_gnomADg_nhomalt_popmax CSQ_gnomADg_popmax", | ||
| "stage-rpt_generate_workbook.acmg": true, | ||
| "stage-rpt_generate_workbook.rename_columns": "CSQ_Feature=Transcript DP_FMT=DP", | ||
| "stage-rpt_generate_workbook.add_comment_column": true, | ||
| "stage-rpt_generate_workbook.keep_tmp": true, | ||
| "stage-rpt_generate_workbook.summary": "dias", | ||
| "stage-rpt_generate_workbook.filter": "bcftools filter -e '(CSQ_Consequence==\"synonymous_variant\" | CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"upstream_gene_variant\" | CSQ_Consequence==\"downstream_gene_variant\" | CSQ_Consequence==\"intergenic_variant\" | CSQ_Consequence==\"5_prime_UTR_variant\" | CSQ_Consequence==\"3_prime_UTR_variant\" | CSQ_gnomADe_AF>0.01 | CSQ_gnomADg_AF>0.01 | CSQ_TWE_AF>0.05) & CSQ_HGMD_CLASS!~ \"DM\" & CSQ_ClinVar_CLNSIG!~ \"pathogenic\\/i\" & CSQ_ClinVar_CLNSIGCONF!~ \"pathogenic\\/i\"'", | ||
| "stage-rpt_generate_workbook.human_filter": "excluded gnomAD exomes / genomes > 1%, TWE > 5%, synonymous / intronic / intergenic / upstream / downstream / UTRs EXCEPT pathogenic status in ClinVar OR DM in HGMD Class", | ||
| "stage-rpt_generate_workbook.reorder_columns": "CHROM POS REF ALT GT GQ DP_FMT AD CSQ_SYMBOL CSQ_EXON CSQ_INTRON CSQ_HGVSc CSQ_HGVSp CSQ_Consequence CSQ_IMPACT CSQ_VARIANT_CLASS CSQ_gnomADe_AF CSQ_gnomADe_Hom CSQ_gnomADe_AC CSQ_gnomADe_AN CSQ_gnomADe_nhomalt CSQ_gnomADg_AF CSQ_gnomADg_AC CSQ_gnomADg_AN CSQ_gnomADg_nhomalt CSQ_TWE_AF CSQ_TWE_AC_Hom CSQ_TWE_AC_Het CSQ_TWE_AN CSQ_HGMD CSQ_HGMD_CLASS CSQ_HGMD_RANKSCORE CSQ_HGMD_PHEN CSQ_Existing_variation CSQ_ClinVar CSQ_ClinVar_CLNDN CSQ_ClinVar_CLNSIG CSQ_Mastermind_MMID3 CSQ_CADD_PHRED CSQ_REVEL CSQ_SpliceAI_pred_DS_AG CSQ_SpliceAI_pred_DS_AL CSQ_SpliceAI_pred_DS_DG CSQ_SpliceAI_pred_DS_DL CSQ_HGVS_OFFSET CSQ_STRAND CSQ_Feature", | ||
| "stage-rpt_generate_workbook.freeze_column": "N2", | ||
| "stage-rpt_athena.exons_file": "INPUT-exonsfile", | ||
| "stage-rpt_athena.limit": 260, | ||
| "stage-rpt_athena.summary": true, | ||
| "stage-rpt_athena.thresholds": "100, 250, 500, 1000, 1500", | ||
| "stage-rpt_athena.cutoff_threshold": 250, | ||
| "stage-rpt_athena.mosdepth_files": { | ||
| "folder": "eggd_mosdepth", | ||
| "name": "per-base.bed.gz$|reference_build.txt$" | ||
| } | ||
| } | ||
| }, | ||
| "artemis": { | ||
| "inputs": { | ||
| "capture_bed": { | ||
| "$dnanexus_link": { | ||
| "project": "project-Fkb6Gkj433GVVvj73J7x8KbV", | ||
| "id": "file-GFPxpJj4GVV0Pfzv4VGYf1pq" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |