dias_CEN_config_GRCh37_v3.1.9.json

This repo contains a JSON config file which is used with eggd_dias_batch to specify inputs for running the Dias pipeline for CEN data.

What does the config do?

eggd_dias_batch (https://github.com/eastgenomics/eggd_dias_batch) is a DNAnexus app that runs the Dias pipeline for germline sequence data analysis. The egg5_dias_CEN_config repo contains the dias_CEN_config file that specifies the executables and their input files to be used in the Dias pipeline for analysing CEN data on build GRCh37.

New versions of apps and app inputs for use in the Dias pipeline can be updated in the config without needing to update the pipeline itself.

Parts of the config

The config specifies app IDs and workflow IDs at the top, followed by a reference_files dict for inputs common to multiple running modes. The modes section specifies inputs specific to a running mode:

cnv_call
- specifies inputs for CNV calling.
snv_reports
- specifies inputs for dias_reports.
cnv_reports
- specifies inputs for dias_cnvreports.
mosaic_reports
- specifies inputs for dias_reports for mosaic reports.
artemis
- specifies inputs for artemis

Versions of workflows, apps, and dynamic files in the config

Workflows:

Dias reports: dias_reports_v2.2.2
- DNAnexus workflow ID: workflow-GkbJY284FpfgqF8ggz57fVY2
Dias CNV reports: dias_cnvreports_v1.2.0
- DNAnexus workflow ID: workflow-Gj77F9041Ky3Vp045gpKx0B4

Apps:

CNV calling app: eggd_GATKgCNV_call
- v1.0.2
- DNAnexus app ID: app-GZ4pXxj4xG062Bj5zjgP1Bb0
Artemis app: eggd_artemis
- v1.5.0
- DNAnexus app ID app-GkbJ7p0463bjk9VKv3x8G5F8

Dynamic files:	File	File name
genepanels	240405_genepanels.tsv	`file-Gj7ygzj42X4ZBqg9068p1fQ4`
exons	GCF_000001405.25_GRCh37.p13_genomic.exon_5bp_v2.0.0.tsv	`file-GF611Z8433Gk7gZ47gypK7ZZ`
genes2transcripts	240402_g2t.tsv	`file-Gj770X8433Gb506pjq1PxXG9`
exons_with_symbols for eggd_athena	GCF_000001405.25_GRCh37.p13_genomic.symbols.exon_5bp_v2.0.0.tsv	`file-GF611Z8433Gf99pBPbJkV7bq`
cen_vep_config for SNV/mosaic reports	cen_vep_config_v1.1.19.json	`file-GqbJJ404z6j62Q5X3qp1G4Xf`
cen_vep_config for CNV reports	cen-cnv_config_v1.1.0.json	`file-GQGJ3Z84xyx0jp1q65K1Q1jY`
panel_dump for eggd_optimised_filtering	240202_panelapp_dump.json	`file-Gg35Vf845B5bV08VqJ0qGV5V`
additional_regions for CNVs	CEN_CNV_additional_regions_b37_v1.0.1.tsv	`file-GJZQvg0433GkyFZg13K6VV6p`
gatk_docker	GATK_v4.2.5.0.tar.gz	`file-GBBP9JQ433GxV97xBpQkzYZx`
interval_list for CNV calling	CEN_CNV_targets_v1.1.0_sorted.interval_list	`file-GFPxzKj4V50pJX3F4vV58yyg`
annotation of interval_list for CNV calling	CEN_CNV_targets_v1.1.0_sorted_annotation.tsv	`file-GFPxzPQ4V50z4pv230p82G0q`
capture_bed for artemis	CEN_CNV_targets_b37_v1.1.0.bed	`file-GFPxpJj4GVV0Pfzv4VGYf1pq`

eastgenomics / egg5_dias_CEN_config

readme

dias_CEN_config_GRCh37_v3.1.9.json

What does the config do?

Parts of the config

Versions of workflows, apps, and dynamic files in the config