dias_TWE_config_GRCh37_v3.1.8.json

This repo contains a JSON config file which is used with eggd_dias_batch to specify inputs for running the Dias pipeline for TWE 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 egg4_dias_TWE_config repo contains the dias_TWE_config file that specifies the executables and their input files to be used in the Dias pipeline for analysing TWE 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 that could be used in multiple running modes. The modes section specifies inputs specific to a running mode. The TWE config currently only has one running mode:

• dias_reports
  • specifies the inputs for dias_reports.
• artemis
  • specifies inputs for artemis

Versions of workflows and dynamic files in the config

Workflows:

• Dias reports: dias_reports_v2.2.2
  • DNAnexus workflow ID: workflow-GkbJY284FpfgqF8ggz57fVY2

Apps:

• Artemis app: eggd_artemis
  • v1.5.0
  • DNAnexus app ID app-GkbJ7p0463bjk9VKv3x8G5F8

Dynamic files:

File	File name	DNAnexus file ID
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
panel_dump for eggd_optimised_filtering	240202_panelapp_dump.json	file-Gg35Vf845B5bV08VqJ0qGV5V
exons_with_symbols for eggd_athena	GCF_000001405.25_GRCh37.p13_genomic.symbols.exon_5bp_v2.0.0.tsv	file-GF611Z8433Gf99pBPbJkV7bq
twe_vep_config for SNV reports	twe_vep_config_v1.1.21.json	file-GvJ0qp04j4fb5b1z6j88QG6v