long-read-pipelines
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broadinstitute
Long read production pipelines
Hi, Here is an issue for pipeline ONTProcessBasecall. If the input fastq data are all failed, the ListFastqs task will terminate directly without an error message saying "No valid input...
https://cloud.google.com/blog/products/storage-data-transfer/new-gcloud-storage-cli-for-your-data-transfers claims it's much more efficient.
`miniwdl check` + shellcheck found many small issues within our repo. - unused tasks - bad shell code practices. We should find a time to resolve most of them.
https://www.nature.com/articles/s41592-022-01432-3
Merging work based on the development I have been working on for the short read malaria project. Most updates are in line with `jts_updates_for_malaria_joint_calling` branch as of 4/23/2024. Major updates:...
**Changes made:** Added -recover_swapped true to the LiftoverVcf command to handle swapped alleles automatically. **Benefits**: Improves the accuracy of allele representation post-liftover. Reduces manual post-processing efforts to correct swapped alleles.
Implemented enhancements to the `ReadMetrics` task, allowing for customizable memory inputs and adding support for SSD. This update will provide better flexibility for allocating memory to the `PerFlowCellMetrics` task. The...
**Overview:** This branch is built on top of [jts_kvg_sp_malaria](https://github.com/broadinstitute/long-read-pipelines/tree/jts_kvg_sp_malaria) branch. This PR improves our BAM file indexing process by ensuring index files are automatically saved alongside BAM files. **Key Updates:**...