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nf-core

129 indexed repositories · View on GitHub

rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Nextflow · 1370 stars
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Nextflow · 603 stars
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!

Nextflow · 429 stars
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl...

Nextflow · 356 stars
tools
Python package with helper tools for the nf-core community.

Python · 322 stars
mag
Assembly and binning of metagenomes

Nextflow · 321 stars
ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nextflow · 260 stars
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.

Nextflow · 246 stars
atacseq
ATAC-seq peak-calling and QC analysis pipeline

Nextflow · 230 stars
nanoseq
Nanopore demultiplexing, QC and alignment pipeline

Nextflow · 230 stars
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Nextflow · 215 stars
fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases

Nextflow · 202 stars
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

Nextflow · 198 stars
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Nextflow · 194 stars
rnafusion
RNA-seq analysis pipeline for detection of gene-fusions

Nextflow · 174 stars
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples

Nextflow · 166 stars
test-datasets
Test data to be used for automated testing with the nf-core pipelines

164 stars
raredisease
Call and score variants from WGS/WES of rare disease patients.

Nextflow · 124 stars
oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline

Nextflow · 121 stars
funcscan
(Meta-)genome screening for functional and natural product gene sequences

Nextflow · 119 stars
109 more repositories live on View on GitHub

Beginner friendly Everything

Open All

Convert UPD bed files to bigBed format Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

nf-core/raredisease#1029 · Opened Sep 16, 2026
Broken link in documentation: [404] Page not found: https://nf-co.re/sarek/3.10.0/docs/output/ Open

bug

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

nf-core/website#4401 · Opened Sep 16, 2026
Docs: run nf-core/taxprofiler's DIAMOND classifier alongside metatdenovo for a complementary community profile Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

nf-core/metatdenovo#518 · Opened Sep 15, 2026
[404] Page not found: https://nf-co.re/images/graphic_design_assets/workflow_schematics_components/generic/nf-core_components.xml Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

nf-core/website#4400 · Opened Sep 15, 2026
Add source `.mmd` for metro map Open

Difficulty 1/5 1-3 hours Newbie friendliness 85/100

nf-core/ncrnannotator#12 · Opened Sep 14, 2026
Syntax mistake in docs Open

Difficulty 1/5 Under an hour Newbie friendliness 82/100

nf-core/smrnaseq#553 · Opened Sep 12, 2026
Documentation update: cutn/targetGenome Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 88/100

nf-core/pairgenomealign#155 · Opened Sep 11, 2026
Docs: use relative cross-doc links now that website#4385 has landed Open

documentation

Difficulty 1/5 Under an hour Newbie friendliness 92/100

nf-core/magmap#249 · Opened Sep 2, 2026
External software version list Open

enhancement

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

nf-core/airrflow#501 · 2 comments · Opened Sep 1, 2026
BAM_MARKDUPLICATES emits duplicate alignment channel under -stub Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

nf-core/sarek#2280 · Opened Aug 31, 2026
Code cleaning (nf-core TODO line) Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/fastqrepair#52 · Opened Aug 31, 2026
The nextflex profile should be updated to fit the v4 library kit Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/smrnaseq#550 · 2 comments · Opened Aug 31, 2026
config parsing failed Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/proteinfold#650 · 1 comment · Opened Aug 31, 2026
AlphaFold3 data pipeline never finds the Rfam database (Rfam-*.fasta glob does not match the shipped filename) Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

nf-core/proteinfold#649 · Opened Aug 28, 2026
add_sh_to_taxonomy.py (--addsh) miscounts rank columns when Species_exact is present Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

nf-core/ampliseq#1064 · Opened Aug 25, 2026
Housekeeping: remove debug println and stray null file Open

area: infra bug good first issue priority: low

Difficulty 1/5 1-3 hours Newbie friendliness 88/100

nf-core/fastqrepair#37 · 1 comment · Opened Aug 22, 2026
Formatting issues when generating container definitions Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

nf-core/tools#4452 · Opened Aug 21, 2026
`-profile conda` fails: `bioconda::biopython=1.84` cannot be resolved Open

Difficulty 2/5 1-3 hours Newbie friendliness 85/100

nf-core/taxmarker#5 · Opened Aug 19, 2026
Action Required: Fix Renovate Configuration Open

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

nf-core/test-datasets#2225 · Opened Aug 19, 2026
Action Required: Fix Renovate Configuration Open

Difficulty 2/5 1-3 hours Newbie friendliness 63/100

nf-core/setup-nf-test#53 · Opened Aug 18, 2026
ToulligQC missing from tools table Open

documentation

Difficulty 1/5 Under an hour Newbie friendliness 70/100

nf-core/seqinspector#273 · Opened Aug 18, 2026
MODKIT_BEDGRAPH produces empty output when pileup run with --combine-mods Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

nf-core/methylong#91 · Opened Aug 17, 2026
Update primer file in genomes config Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

nf-core/viralrecon#614 · Opened Aug 14, 2026
update module: cellranger Open

update module

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/modules#12660 · 1 comment · Opened Aug 12, 2026
Generated mag samplesheet is rejected by mag 5.5.0: empty `group`, missing `short_reads_platform` Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

nf-core/detaxizer#100 · Opened Aug 11, 2026
filter.nf: `$(COUNTER-1)` should be `$((COUNTER-1))` Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

nf-core/detaxizer#99 · 2 comments · Opened Aug 11, 2026
Document potential differences in annotation tool version Open

bug

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

nf-core/magmap#229 · Opened Aug 4, 2026
Rename branch name `master` to `main` Open

enhancement

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

nf-core/bacass#321 · Opened Jul 29, 2026
More details to specifications/pipelines/requirements/workflow_specificity page Open

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

nf-core/website#4320 · 1 comment · 1 reaction · Opened Jul 23, 2026
Pipeline not using fasta from igenomes Open

bug

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

nf-core/raredisease#934 · 1 comment · Opened Jul 17, 2026
MCQUANT falsely fails "channels don't match" on large images Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/mcmicro#163 · Opened Jul 16, 2026
PRELUDE summary steps never cache on -resume (expensive on AWS Batch) Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/mcmicro#162 · Opened Jul 16, 2026
[404] Page not found: https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

nf-core/test-datasets#2144 · Opened Jul 13, 2026
SEQTK_SAMPLE fails on `.fq.gz` inputs — output glob `*.fastq.gz` misses the preserved input extension Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

nf-core/seqinspector#254 · Opened Jul 13, 2026
Issue with STAR version that produced segmentation faults. Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/cageseq#111 · 1 reaction · Opened Jul 10, 2026
MUSE channel cardinality Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/sarek#2224 · Opened Jun 29, 2026
Malformed STAR --outSAMattrRGline due to incorrect whitespace in PL tag Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 82/100

nf-core/rnafusion#822 · Opened Jun 26, 2026
Consider enforcing line feeds in .gitattributes Open

enhancement

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

nf-core/tools#4341 · Opened Jun 23, 2026
Incorrect if-statement logic in nf-core modules test output Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/tools#4327 · 4 comments · Opened Jun 16, 2026
[404] Page not found: https://nf-co.re/docs/contributing/sync Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/website#4255 · Opened Jun 12, 2026
Anndata var_names Not Set Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

nf-core/molkart#135 · 2 comments · Opened Jun 4, 2026
QUANT: silent per-sample drop from order-dependent combine(by:) on groupKey Open

bug

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

nf-core/mhcquant#459 · Opened Jun 3, 2026
[404] Page not found: https://training.nextflow.io/ Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 75/100

nf-core/website#4243 · Opened Jun 1, 2026
The Usage section said use tab-delimited file but the samplesheet is actually comma-delimited Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 78/100

nf-core/atacseq#444 · Opened May 31, 2026
[upgrade] Proseg: bump v3.1.0 → v3.1.1 (patch release) Open

Difficulty 2/5 Half a day Newbie friendliness 76/100

nf-core/spatialaxe#169 · Opened May 28, 2026
MSIsensorPro output file name mismatch? Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/sarek#2192 · 1 comment · Opened May 24, 2026
FilterMutectCalls --stats parameter Open

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

nf-core/sarek#2191 · 3 comments · Opened May 24, 2026
Min Quality differes between iVar and mpileup Open

bug good first issue

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/viralrecon#598 · Opened May 18, 2026
[404] Page not found: https://nf-co.re/docs/nf-core-tools/cli/subworkflows/create Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/website#4208 · 2 comments · Opened May 11, 2026
bwameth symlink bug Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/methylseq#608 · 6 comments · Opened May 6, 2026

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