WDL to run feature extract, VQSR, and upload #6966
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| cat ~{filter_set_name}.snps.recal.tsv ~{filter_set_name}.indels.recal.tsv | grep -v filter_set_name | grep -v "#" > filter_set_load.tsv | ||
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| # BQ load likes a : instead of a . after the project | ||
| bq_info_table=$(echo ~{fq_info_destination_table} | sed s/\\./:/) |
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that's weird that you need a : after the project. in our other scripts, we specify the project with --project_id=~{project_id} and then we don't include it in the dataset.table. also, when i was doing a bq query, the : was needed when i was using legacy mode and the . otherwise.
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yeah you can supply the default project with --project_id OR can you supply a fully qualified name. Since for all the other scripts we tend to take in a FQ table name (project.dataset.table) I kept this the same from an input perspective for user consistency, but that means we have to fiddle it here to get it in the right format for bq load
| disk_size = large_disk | ||
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| call SNPsVariantRecalibrator as SNPsVariantRecalibratorClassic { |
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nit - we could remove the as here (i'm guessing we used to have a classic and non classic mode)
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yeah -- I think we're going to have a "non-classic" mode as well once we start scale testing. The WARP pipeline has it for > 10k wgs samples... but it's a bunch of logic. Happy to remove the "as ..." for now though
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| df -h | ||
| min_location=$(echo "~{chrom_id} * ~{chrom_offset}" | bc) | ||
| max_location=$(echo "( ~{chrom_id} + 1 ) * ~{chrom_offset}" | bc) |
* WDL to run feature extract, VQSR, and upload * PR feedback
* WDL to run feature extract, VQSR, and upload * PR feedback
* WDL to run feature extract, VQSR, and upload * PR feedback
* WDL to run feature extract, VQSR, and upload * PR feedback
* WDL to run feature extract, VQSR, and upload * PR feedback
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