nf-core/eager

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A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Stars: 215
Forks: 91
Open beginner issues: 0
Indexed issues: 56
Avg merge: 5m
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

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56 open issues indexed

DSL2: MAPAD parameters Open

bug DSL2

nf-core/eager#1194 · 2 comments · 1 assignee · Opened Sep 18, 2026
DSL2: `-resume` unsuccessful caching of some processes Open

bug DSL2

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nf-core/eager#1193 · Opened Sep 18, 2026
DSL2: Host removal is never actually ran Open

bug DSL2

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/eager#1189 · Opened Sep 11, 2026
DSL2: Reference indexing result directory structure does not match output.md Open

bug documentation DSL2

Difficulty 3/5 1-2 days Newbie friendliness 62/100

nf-core/eager#1187 · 1 comment · Opened Sep 4, 2026
DSL2: mapdamage appears in multiqc, even when it is not run Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/eager#1179 · Opened Jul 3, 2026
DSL2: bamqc does not get stats across all references in multi-ref cases Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/eager#1178 · Opened Jul 3, 2026
DSL2: Processed reads not saved in results directory Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/eager#1176 · Opened Jun 8, 2026
DSL2: Add option for polyG/X trimming with fastp Open

DSL2 enhancement

nf-core/eager#1175 · 1 comment · 1 assignee · Opened Jun 8, 2026
DSL2: Duplicate module configurations in modules.conf Open

DSL2

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/eager#1173 · 2 comments · Opened Apr 17, 2026
DSL2: Pre-Release Checklist Open

DSL2

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#1172 · Opened Apr 10, 2026
DSL2: Update modules to use version topics Open

DSL2 help wanted needs upstream fix

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

nf-core/eager#1170 · Opened Mar 17, 2026
terminated with an error exit status (140) Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/eager#1166 · 4 comments · Opened Nov 26, 2025
DSL2: ATLAS genotyping Open

DSL2 enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#1165 · Opened Nov 20, 2025
Using modified strobealign to align ancient DNA Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/eager#1160 · 6 comments · Opened Oct 4, 2025
DSL2: Switch to `main` branch Open

easier-tasks major

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nf-core/eager#1157 · Opened Aug 22, 2025
DSL2: bwa index with multiref may be overwriting each other Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/eager#1152 · 1 comment · Opened Jun 26, 2025
DSL2: metagenomics modules config for krakenuniq duplicated Open

bug

nf-core/eager#1150 · 1 assignee · Opened Jun 6, 2025
DSL2: `test_full` nf-test conversion Open

DSL2

nf-core/eager#1141 · 1 assignee · Opened May 2, 2025
Variation graph mapping Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#1132 · 3 comments · Opened Apr 14, 2025
DSL2 - Host-removal keeps adapters in [DISCUSSION?] Open

DSL2

nf-core/eager#1131 · 1 comment · 1 assignee · Opened Apr 11, 2025
DSL2 remove or change bamfiltering_genomicbamfilterflag Open

bug DSL2

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/eager#1130 · Opened Apr 11, 2025
DSL2 - Genotyping on unmerged libraries Open

DSL2 enhancement

nf-core/eager#1128 · 4 comments · 1 assignee · Opened Mar 26, 2025
[test data] Human aligned bam testdataset still has SQ tags for non-existant fasta indices in corresponding fasta used Open

bug needs upstream fix

nf-core/eager#1127 · 1 assignee · Opened Mar 26, 2025
JSON schema: Eager Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/eager#1124 · Opened Mar 25, 2025
DSL2: test_nothing profile is broken Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 20/100

nf-core/eager#1117 · 1 comment · Opened Feb 21, 2025
Edit distance plots for mapped reads Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/eager#1101 · 1 comment · Opened Dec 6, 2024
DSL2: Options for different adapters for ssDNA and dsDNA libraries within the same run. Open

DSL2 enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/eager#1091 · 1 comment · Opened Oct 1, 2024
DSL2: Add bamRefine as a damage manipulation alternative? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/eager#1087 · 1 comment · Opened Sep 19, 2024
DSL2: Genotyping on multiple snp sets in one run? Open

DSL2 enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/eager#1077 · 1 comment · Opened Jun 21, 2024
DSL2: Add 'output' documention for mtnucratio Open

documentation DSL2

Difficulty 1/5 Under an hour Newbie friendliness 85/100

nf-core/eager#1070 · Opened May 17, 2024
DSL2: Add MultiVCFAnalyzer Open

DSL2 enhancement

nf-core/eager#1069 · 2 comments · 1 assignee · Opened May 17, 2024
DSL2: Ensure modules config consistency: all modules have an `ext.prefix` and `publishDir` attribute, and follow conventions. Open

DSL2

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/eager#1066 · Opened Apr 26, 2024
Fix description of mt/n ratio in docs Open

documentation DSL1 DSL2

Difficulty 1/5 Under an hour Newbie friendliness 52/100

nf-core/eager#1055 · Opened Feb 28, 2024
Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed Open

DSL2

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/eager#1054 · Opened Feb 23, 2024
DSL2: Add HapCON? Open

DSL2 enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/eager#1015 · Opened Jul 21, 2023
DSL2: Add to MultiQC support for coverage_across_reference.txt file Open

DSL2 enhancement needs upstream fix

Difficulty 3/5 1-2 days Newbie friendliness 20/100

nf-core/eager#1001 · Opened Jun 23, 2023
DSL2: Print Nuclear Contamination JSON `N/A` value Open

bug DSL2

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/eager#995 · 2 comments · Opened Jun 7, 2023
DSL2: PMDTools for estimation vs manipulation of damage Open

DSL2

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/eager#989 · Opened May 26, 2023
DSL2: Add test profile that forces ALL the possible merging steps for FastQ and BAM inputs, to ensure no file name collisions happen. Open

DSL2

nf-core/eager#986 · 1 comment · 1 assignee · Opened May 25, 2023
DSL2: Provide correct data for upload to sequencing archives (e.g. ENA) Open

DSL2 enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#974 · Opened May 2, 2023
DSL2L: Add support for specifying platform in input TSV Open

DSL2 enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/eager#970 · Opened Apr 21, 2023
Possiblity to extract non-host paired-end reads in separate FastQ files Open

DSL2 enhancement

nf-core/eager#945 · 1 assignee · Opened Feb 22, 2023
DSL2: Document loudly that -params-files should replace custom.config for parameters Open

DSL2 enhancement

Difficulty 1/5 Under an hour Newbie friendliness 38/100

nf-core/eager#943 · Opened Jan 25, 2023
DSL2: pop-gen Open

DSL2 enhancement

nf-core/eager#924 · 3 assignees · Opened Oct 7, 2022
DSL2: stats Open

DSL2 enhancement

nf-core/eager#922 · 1 comment · 1 assignee · Opened Oct 7, 2022
Dev notes: eager3 don't forget list Open

DSL2

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/eager#918 · Opened Sep 11, 2022
Mitochondrial and Ych haplotype callers Open

DSL2 enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#917 · 7 comments · Opened Sep 6, 2022
DSL2: Sex determination output sometimes listed on Sample, sometimes on library level Open

bug DSL2

nf-core/eager#837 · 2 comments · 1 assignee · Opened Mar 4, 2022
DSL2: Only load modules if being used Open

DSL2 enhancement low_priority

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/eager#830 · 7 comments · Opened Feb 2, 2022
DSL2 Planning Open

DSL2 enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/eager#778 · 5 comments · Opened Jul 14, 2021

nf-core/eager

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