long-read-pipelines
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broadinstitute
Long read production pipelines
And various cleanups. Tested working with a 6-FC sample (to see if the source allocation is too frugal).
tested working https://app.terra.bio/#workspaces/production-long-reads/broad-gp-pacbio/job_history/40533c3c-9e1d-47a7-ab47-8664ef0d88bc
Integrated Sniffles2 to CallVariantsPBCCS.wdl. Test ran on sample HG00514. Sniffles2 will call variants across the whole genome only since the .snf files can't be merged.
- Adding in tasks for pulling out sub-regions and updating main wdl. - Adding in wdl for Transcript Isoform Analysis. - Updated 10x Array pipeline for wider sharding. - Added...
Script to automate data delivery from our production workspaces to delivery workspaces in Terra.
From @SHuang-Broad: One potential issue: currently the version of samtools in the environment.yml is 1.10. Here it's being updated to 1.11. I'd vote for removing the samtools in the yaml...