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maintain sample order in GEM output

enhancement

Status: Open.

#292 In SystemsGenetics/GEMmaker;

· hharg910 opened on Mar 17, 2026

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

bug

Status: Open.

#291 In SystemsGenetics/GEMmaker;

· Huiting120 opened on Nov 13, 2025

Automatic cleanup with nf-boost

Status: Open.

#289 In SystemsGenetics/GEMmaker;

· bentsherman opened on Apr 25, 2024

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

bug

Status: Open.

#287 In SystemsGenetics/GEMmaker;

· JohnHadish opened on Feb 2, 2024

MultiQC for STAR alignment incorrect

bug

Status: Open.

#285 In SystemsGenetics/GEMmaker;

· Huiting120 opened on Jan 9, 2024

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

bug

Status: Open.

#280 In SystemsGenetics/GEMmaker;

· JohnHadish opened on Aug 18, 2023

GEMmaker documentation--using gffread to make GTF file

bug

Status: Open.

#278 In SystemsGenetics/GEMmaker;

· ko0000 opened on Apr 15, 2023

create_gem rewrite with join

enhancement

Status: Open.

#273 In SystemsGenetics/GEMmaker;

· JohnHadish opened on Jan 18, 2023

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

bug

Status: Open.

#266 In SystemsGenetics/GEMmaker;

· JohnHadish opened on Nov 14, 2022

Documentation Fixes

documentation

Status: Open.

#264 In SystemsGenetics/GEMmaker;

· spficklin opened on Oct 21, 2022

Updates to docs

documentation

Status: Open.

#260 In SystemsGenetics/GEMmaker;

· spficklin opened on Mar 16, 2022

Samtool "% Mapped" is unneccesary

enhancement

Status: Open.

#256 In SystemsGenetics/GEMmaker;

· JohnHadish opened on Jan 29, 2022