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Published July 16, 2021 | Version v5.0.0
Software Open

biowdl/RNA-seq: Release 5.0.0

Creators

  • 1. @LUMC
  • 2. Leiden University Medical Center
  • 3. Leiden University Medical Center (LUMC)
  • 4. LUMC

Description

  • Update default CPAT version to 3.0.4.
  • Use gffcompare to merge stringtie assembly GTF files, rather than stringtie merge.
  • Add call to create annotation file for shiny app.
  • Add call to create design matrix template for shiny app.
  • Add predex v0.9.2 container to dockerImages.
  • dockerImages.yml: update umitools (v1.1.1) image with correct version of samtools (1.10).
  • test/cromwell_options.json: add memory attribute.
  • dockerImages.yml: update umitools to version 1.1.1 (multi-package including samtools).
  • Replace travis with github CI.
  • Add the dockerImages to the output section.
  • Make running stringtie optional by exposing the boolean runStringtieQuantification.
  • Downgrade stringtie to version 1.3.6, as version 2 returns unstranded transcripts which is incompatible with htseq-count.
  • When multiple TPM/FPKM values are returned for a single gene by stringtie, they will now be added together in the multi-sample expression tables. Previously only the last value encountered would be used.
  • Updated default docker image for collect-columns (now uses version 1.0.0 instead of 0.2.0).

Files

biowdl/RNA-seq-v5.0.0.zip

Files (4.6 MB)

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md5:435b2f9d15a9ee8fada4724536d899f1
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Additional details

Related works

Is supplement to
https://github.com/biowdl/RNA-seq/tree/v5.0.0 (URL)