long-read-pipelines
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broadinstitute
Long read production pipelines
https://github.com/broadinstitute/long-read-pipelines/blob/9620d58f49f29dd2f27fa5f30f72c8257aa2064b/docker/lr-metrics/Dockerfile#L22 We should do better.
User feedback.
- [ ] `ONT/Epigenomics/ONTMethylation.wdl` - [ ] `TechAgnostic/VariantCalling/LRCNVs.wdl` I'll also document the touched dockers.
Some docker images are stored in either quay or docker hub, these should be migrated to google artifact register for consistency. Example : quay.io/broad-long-read-pipelines/lr-pacasus
I am trying to run a long read pipeline with ONT long reads data for mouse models using Terra platform. I was able to run https://github.com/broadinstitute/long-read-pipelines/blob/kvg_guppy_cpu/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl successfully using my fast5...
More than just `womtool validate`
The current LRConvertBCF workflow, is used to convert a BCF file into a compressed VCF file, and is intended as a temporary solution to handle transient issues. It needs to...
I was using some tasks from here: https://github.com/broadinstitute/long-read-pipelines/blob/dc2cd65fe18e9301925f88cc79a3db601cd38029/wdl/tasks/Utility/Finalize.wdl (specifically FinalizeToDir) and I ran into some esoteric cases where call-caching was failing to re-upload results even when the underlying files had...
Added an optional parameter length_threshold. From minimap2 Github page: "paftools.js call ignores alignments 50kb or shorter; when deriving callable regions, it ignores alignments 10kb or shorter". For mitochondria variant calling,...
updated Dockerfile and Makefile for Canu2.2 version update. added "technology" parameter in Canu.wdl to specify nanopore vs pacbio sequencing method