Issues

• DSL2: -resume unsuccessful caching of some processes

  bugDSL2
  nf-core/eager#1193 · Filter by author TCLamnidis opened on Sep 18, 2026

• DSL2: Host removal is never actually ran

  bugDSL2
  nf-core/eager#1189 · Filter by author TCLamnidis opened on Sep 11, 2026

• DSL2: Reference indexing result directory structure does not match output.md

  bugdocumentationDSL2
  nf-core/eager#1187 · Filter by author TCLamnidis opened on Sep 4, 2026
  1

• DSL2: mapdamage appears in multiqc, even when it is not run

  bug
  nf-core/eager#1179 · Filter by author ilight1542 opened on Jul 3, 2026

• DSL2: bamqc does not get stats across all references in multi-ref cases

  bug
  nf-core/eager#1178 · Filter by author ilight1542 opened on Jul 3, 2026

• DSL2: Processed reads not saved in results directory

  bug
  nf-core/eager#1176 · Filter by author DeondeJager opened on Jun 8, 2026

• DSL2: Add option for polyG/X trimming with fastp

  DSL2enhancement
  nf-core/eager#1175 · Filter by author DeondeJager opened on Jun 8, 2026
  1

  

• DSL2: Duplicate module configurations in modules.conf

  DSL2
  nf-core/eager#1173 · Filter by author TCLamnidis opened on Apr 17, 2026
  2

  

• DSL2: Pre-Release Checklist

  DSL2
  nf-core/eager#1172 · Filter by author TCLamnidis opened on Apr 10, 2026

• DSL2: Update modules to use version topics

  DSL2help wantedneeds upstream fix
  nf-core/eager#1170 · Filter by author TCLamnidis opened on Mar 17, 2026

• terminated with an error exit status (140)

  bug
  nf-core/eager#1166 · Filter by author Shaileshdesai76 opened on Nov 26, 2025
  4

• DSL2: ATLAS genotyping

  DSL2enhancement
  nf-core/eager#1165 · Filter by author TCLamnidis opened on Nov 20, 2025

• Using modified strobealign to align ancient DNA

  enhancement
  nf-core/eager#1160 · Filter by author teepean opened on Oct 4, 2025
  6

• DSL2: Switch to main branch

  easier-tasksmajor
  nf-core/eager#1157 · Filter by author TCLamnidis opened on Aug 22, 2025 · 3.0 Augsburg

• DSL2: bwa index with multiref may be overwriting each other

  bug
  nf-core/eager#1152 · Filter by author jfy133 opened on Jun 26, 2025
  1

• DSL2: metagenomics modules config for krakenuniq duplicated

  bug
  nf-core/eager#1150 · Filter by author ilight1542 opened on Jun 6, 2025
  

• DSL2: test_full nf-test conversion

  DSL2
  nf-core/eager#1141 · Filter by author TCLamnidis opened on May 2, 2025
  

• Variation graph mapping

  enhancement
  nf-core/eager#1132 · Filter by author mattiassherman opened on Apr 14, 2025
  3

• DSL2 - Host-removal keeps adapters in [DISCUSSION?]

  DSL2
  nf-core/eager#1131 · Filter by author merszym opened on Apr 11, 2025 · 3.0 Augsburg
  1

  

• DSL2 remove or change bamfiltering_genomicbamfilterflag

  bugDSL2
  nf-core/eager#1130 · Filter by author merszym opened on Apr 11, 2025 · 3.0 Augsburg

• DSL2 - Genotyping on unmerged libraries

  DSL2enhancement
  nf-core/eager#1128 · Filter by author ilight1542 opened on Mar 26, 2025
  4

  

• [test data] Human aligned bam testdataset still has SQ tags for non-existant fasta indices in corresponding fasta used

  bugneeds upstream fix
  nf-core/eager#1127 · Filter by author ilight1542 opened on Mar 26, 2025
  

• JSON schema: Eager

  documentation
  nf-core/eager#1124 · Filter by author jen-reeve opened on Mar 25, 2025

• DSL2: test_nothing profile is broken

  bug
  nf-core/eager#1117 · Filter by author TCLamnidis opened on Feb 21, 2025
  1

• Edit distance plots for mapped reads

  enhancement
  nf-core/eager#1101 · Filter by author marcel-keller opened on Dec 6, 2024
  1