Caution

This repo contains a JSON file (compatible with new eggd_dias_batch - planned to go live in Jan 2024) and a Python script (compatible with old dias_batch - currently being used)

The readme.md describes the JSON not the python script

When new eggd_dias_batch goes live the python script will be deleted

dias_TWE_config_GRCh37_v3.0.1.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/dias_batch_running) is a DNAnexus app that runs the Dias pipeline for germline sequence data analysis. The egg5_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.

Versions of workflows and dynamic files in the config

Workflows:

• Dias reports: dias_reports_v2.1.0
  • DNAnexus workflow ID: workflow-GXzkfYj4QPQp9z4Jz4BF09y6

Dynamic files:

File	File name	DNAnexus file ID
genepanels	230602_genepanels.tsv	file-GVx0vkQ433Gvq63k1Kj4Y562
exons_nirvana	GCF_000001405.25_GRCh37.p13_genomic.exon_5bp_v2.0.0.tsv	file-GF611Z8433Gk7gZ47gypK7ZZ
genes2transcripts	230421_g2t.tsv	file-GV4P970433Gj6812zGVBZvB4
exons_file 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_v1.1.11.json	file-Gf0q8fj4j4fZG84VJ9YYvKVk