Trans eQTL runner - #263
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Pull Request Overview
This PR updates the trans eQTL runner by removing the --regions option so that all variants in the VCF are processed. Additionally, it introduces a new configuration file and updates the runner script to align with that change.
- Added new configuration settings in trans_associatr_runner.toml.
- Updated the runner script to no longer pass --regions to associaTR.
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| str/trans-eqtl/trans_associatr_runner.toml | Added new configuration options without the --regions parameter. |
| str/trans-eqtl/trans_associatr_runner.py | Updated the job command and concurrency handling logic to support processing all variants. |
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Is there a way to bypass the Ubuntu image check or do I have to update the image? |
| Run associaTR processing pipeline | ||
| """ | ||
| b = get_batch(name='Run associatr') | ||
| init_batch() |
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I don't think this is needed here? init_batch starts a hail query runtime, but you only need a batch
| vcf_file_path = get_config()['associatr']['vcf_file_path'] | ||
| variant_vcf = b.read_input_group( | ||
| **dict( | ||
| base=vcf_file_path, | ||
| ), | ||
| ) |
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this can be moved outside the loops, the VCF isn't specific to celltypes or chromosomes
| import hailtop.batch as hb | ||
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| from cpg_utils import to_path | ||
| from cpg_utils.config import get_config |
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you might want to use config_retrieve, the syntax is a little cleaner, and has built-in informative error messaging if you try and access keys which don't exist, e.g.
get_config()['associatr']['celltypes']
vs.
config_retrieve(['associatr', 'celltypes'])
Remove --regions so that it runs all variants in the vcf.