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XPRESSpipe-v0.5.0

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@j-berg j-berg released this 30 Mar 16:29
XPRESSpipe-v0.5.0
1fc9a93
  • Fixed issue where genome size calculation would round up and miscalculate genome_size parameter for STAR.
  • Added fastp_lite for removal of 3' internal UMIs (generally takes ~1 min per RNA-seq sample with about 30 million reads)
  • For example: 5'-read-spacer-UMI-adapter-3'
    • Integrating this addition into options and trimming
  • Updated MANIFEST file to reliably copy R and Julia scripts to executing folder for XPRESSpipe
  • Updated command builder (xpresspipe build) to include recent additions
  • Updated requirements to prevent issue where solved environment required to install R 3.5.1 or greater would create an error where samtools markdup would freeze
  • Frequently, R 3.5.1 or greater would create library linking error to stringi, causing GenomicFeatures to not function. Added to RbuildIndex.r to reinstall stringi, which appears to clear up the issue.

Most recent working conda environment dependencies: freeze_v0.5.0.txt

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