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
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.
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.
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.
Workflows:
- Dias reports: dias_reports_v2.1.0
- DNAnexus workflow ID:
workflow-GXzkfYj4QPQp9z4Jz4BF09y6
- DNAnexus workflow ID:
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 |