Issues

• --extra_trimgalore_args parsing causes duplicates for valueless flags

  bug
  Bug

  nf-core/rnaseq#1967 · Filter by author jaredfischbach opened on Oct 1, 2026
  1

  

• Option to fail (not silently downgrade) samples with undetermined strandedness

  nf-core/rnaseq#1965 · Filter by author pinin4fjords opened on Sep 30, 2026

• DUPRADAR: featureCounts writes its paired-end temp files into the task work directory (tmpDir = "."), slow on shared/object-storage work dirs

  nf-core/rnaseq#1962 · Filter by author pditommaso opened on Sep 26, 2026

• star_rsem full-size tests: RSEM_CALCULATEEXPRESSION hit its 16 h limit in 3.22.1 and 3.23.0–3.25.0; in three of the four, stdout ends on an rsem-parse-alignments progress line

  nf-core/rnaseq#1957 · Filter by author OtoYuki opened on Sep 25, 2026
  2

• SortMeRNA index built twice; strandedness Salmon index not built centrally

  nf-core/rnaseq#1955 · Filter by author pinin4fjords opened on Sep 25, 2026

• with_umi: transcriptome-side samtools stats silently collide with genome-side (config include order bug)

  nf-core/rnaseq#1941 · Filter by author pinin4fjords opened on Sep 24, 2026

• HISAT2 alignments bypass --min_mapped_reads filtering

  nf-core/rnaseq#1940 · Filter by author pinin4fjords opened on Sep 24, 2026

• Workflow outputs, phase 3: static types for the record boundaries

  nf-core/rnaseq#1935 · Filter by author pinin4fjords opened on Sep 23, 2026

• Workflow outputs, phase 2: replace publishDir with publish: / output {}

  nf-core/rnaseq#1934 · Filter by author pinin4fjords opened on Sep 23, 2026
  1

• Workflow outputs, phase 1: emit per-sample result records from every stage

  nf-core/rnaseq#1933 · Filter by author pinin4fjords opened on Sep 23, 2026

• Migrate to Nextflow workflow outputs via per-stage result records (tracking issue)

  nf-core/rnaseq#1931 · Filter by author pinin4fjords opened on Sep 23, 2026
  1

• Adopt the docker_arm/singularity_arm container-config profile scheme, retire conf/arm.config

  nf-core/rnaseq#1920 · Filter by author pinin4fjords opened on Sep 16, 2026
  3

• Reorganise usage docs with a user-centric structure

  documentation
  nf-core/rnaseq#1737 · Filter by author pinin4fjords opened on Feb 27, 2026

• More than 1 reference genome

  enhancement
  nf-core/rnaseq#1695 · Filter by author gfill88 opened on Feb 9, 2026
  1

• Sylph Performance Improvement

  enhancement
  nf-core/rnaseq#1670 · Filter by author egreenberg7 opened on Dec 19, 2025

• NFCORE_RNASEQ takes values from global scope

  nf-core/rnaseq#1339 · Filter by author adamrtalbot opened on Jul 9, 2024

• Stubs all the way down

  enhancement
  nf-core/rnaseq#1338 · Filter by author maxulysse opened on Jul 9, 2024
  1

• Explicit subsampling step in rnaseq pipeline

  enhancement
  nf-core/rnaseq#1097 · Filter by author ewallace opened on Oct 17, 2023
  2

• Turn off quantification flag

  enhancement
  nf-core/rnaseq#1089 · Filter by author adamrtalbot opened on Oct 10, 2023
  1

• Parameter for using the --save_reference 'genome' directory

  awaiting-response-developersenhancementneeds-testing
  nf-core/rnaseq#998 · Filter by author kaboroevich opened on Apr 11, 2023 · 3.23.0
  4

• Use mudskipper to project HISAT2 genomic alignment onto transcriptome

  enhancement
  nf-core/rnaseq#822 · Filter by author drpatelh opened on May 3, 2022
  3

• Output CRAM as default

  enhancement
  nf-core/rnaseq#758 · Filter by author ewels opened on Jan 31, 2022
  4

• Add detected genes into summary table of MultiQC report

  enhancement
  nf-core/rnaseq#609 · Filter by author ChristopherBarrington opened on Apr 26, 2021
  1

• Show good / bad examples in documentation

  documentation
  nf-core/rnaseq#69 · Filter by author ewels opened on Aug 20, 2018
  6