Issues

• maintain sample order in GEM output

  enhancement
  SystemsGenetics/GEMmaker#292 · Filter by author hharg910 opened on Mar 17, 2026

• If input file is wrong, GEMmaker does not terminate or report the error

  bug
  SystemsGenetics/GEMmaker#291 · Filter by author Huiting120 opened on Nov 13, 2025

• Automatic cleanup with nf-boost

  SystemsGenetics/GEMmaker#289 · Filter by author bentsherman opened on Apr 25, 2024

• Stringtie prepDE.py script does not take sequence length into consideration

  bug
  SystemsGenetics/GEMmaker#287 · Filter by author JohnHadish opened on Feb 2, 2024
  1

• MultiQC for STAR alignment incorrect

  bug
  SystemsGenetics/GEMmaker#285 · Filter by author Huiting120 opened on Jan 9, 2024
  1

• Running local files through trimmomatic fails if file does not end with ".fastq" (e.g. ."fq")

  bug
  SystemsGenetics/GEMmaker#280 · Filter by author JohnHadish opened on Aug 18, 2023
  2

• GEMmaker documentation--using gffread to make GTF file

  bug
  SystemsGenetics/GEMmaker#278 · Filter by author ko0000 opened on Apr 15, 2023

• create_gem rewrite with join

  enhancement
  SystemsGenetics/GEMmaker#273 · Filter by author JohnHadish opened on Jan 18, 2023

• StringTie prepDE.py script needs length argument for calculating raw counts

  bug
  SystemsGenetics/GEMmaker#266 · Filter by author JohnHadish opened on Nov 14, 2022
  1

• Documentation Fixes

  documentation
  SystemsGenetics/GEMmaker#264 · Filter by author spficklin opened on Oct 21, 2022

• Updates to docs

  documentation
  SystemsGenetics/GEMmaker#260 · Filter by author spficklin opened on Mar 16, 2022

• Samtool "% Mapped" is unneccesary

  enhancement
  SystemsGenetics/GEMmaker#256 · Filter by author JohnHadish opened on Jan 29, 2022

• Support for larger genomes

  bugenhancementneeds fix
  SystemsGenetics/GEMmaker#239 · Filter by author fmobegi opened on Jul 23, 2021
  4