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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
nanoseq
Nanopore demultiplexing, QC and alignment pipeline

Nextflow · 230 stars
atacseq
ATAC-seq peak-calling and QC analysis pipeline

Nextflow · 229 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

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KrakenUniq: Passing args to taxprofiler Open

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

nf-core/taxprofiler#772 · Opened Sep 19, 2026
No test covers --cluster_min_seq_id off its default Open

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

nf-core/metatdenovo#533 · Opened Sep 19, 2026
Sixteen local modules use the pre-Apptainer container guard Open

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

nf-core/metatdenovo#531 · 1 comment · Opened Sep 19, 2026
Lint: warn when a docs page will not be rendered on the website Open

nf-core/tools#4474 · 1 assignee · Opened Sep 19, 2026
Spec says additional docs pages are rendered automatically; only docs/usage/ and docs/output/ actually are Open

nf-core/website#4408 · 1 assignee · Opened Sep 19, 2026
[FEATURE] polyglot runtime and publishable Distroless image Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/modules#12997 · Opened Sep 19, 2026
DSL2: MAPAD parameters Open

bug DSL2

nf-core/eager#1194 · 2 comments · 1 assignee · Opened Sep 18, 2026
BUSCO batch mode leaks lineage state between bins: bin_summary.tsv mixes odb10/odb12.2, mislabels domains and misaligns columns Open

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

nf-core/mag#1115 · 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
parse_dada2_taxonomy.r puts non-rank content into the QIIME2 taxonomy string: literal "NA" for all-empty ranks, and SH as an extra rank Open

nf-core/ampliseq#1075 · 1 assignee · Opened Sep 18, 2026
DSL2 port? Open

enhancement

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

nf-core/clipseq#180 · Opened Sep 18, 2026
Run raxtax prefilter before alignment, not after Open

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

nf-core/taxmarker#21 · Opened Sep 18, 2026
SUMMARY_REPORT fails with input file name collision when user-supplied paths share a basename Open

nf-core/ampliseq#1073 · 1 assignee · Opened Sep 17, 2026
Error downloading fusion_report Reference Open

bug

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

nf-core/rnafusion#828 · Opened Sep 17, 2026
Stricter handling of nf-test outputs Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/nft-utils#92 · 1 comment · Opened Sep 17, 2026
aws credentials Open

bug

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

nf-core/scrnaseq#580 · Opened Sep 17, 2026
Lightweight container to avoid pip installing MultiQC Open

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

nf-core/proteinfold#654 · Opened Sep 17, 2026
Check species identifier with g:Profiler API beforehand Open

bug

nf-core/stableexpression#38 · 1 assignee · Opened Sep 16, 2026
Increase default allowed time for `IMPUTE_MISSING_VALUES` module Open

bug

nf-core/stableexpression#37 · 1 assignee · Opened Sep 16, 2026
Check adequacy of gene IDs between g:Profiler output and downloaded Ensembl annotation Open

bug

nf-core/stableexpression#36 · 1 assignee · Opened Sep 16, 2026
Check species name at the very beginning of the pipeline using the NCBI Datasets API Open

enhancement

nf-core/stableexpression#35 · 1 assignee · Opened Sep 16, 2026
update module: SHOVILL Open

update module

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

nf-core/modules#12980 · Opened Sep 16, 2026
Consider adding ViralConsensus Open

enhancement priority

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

nf-core/viralmetagenome#330 · 3 comments · Opened Sep 16, 2026
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
Migrate salmon 1.10.3 -> 2.7.0 (Rust rewrite): validation status and remaining work Open

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

nf-core/rnaseq#1921 · Opened Sep 16, 2026
Adopt the docker_arm/singularity_arm container-config profile scheme, retire conf/arm.config Open

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

nf-core/rnaseq#1920 · 1 comment · 1 reaction · Opened Sep 16, 2026
Reduce privileged-token exposure in fix_linting.yml Open

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

nf-core/tools#4471 · 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
Clean up reporting module Open

help wanted

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

nf-core/genomeassembler#229 · Opened Sep 16, 2026
final MultiQC taking a lot of memory yet not finished Open

bug

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

nf-core/drop#123 · Opened Sep 16, 2026
Consider contributing snpsift_extractfields module to nf-core/modules Open

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

nf-core/viralmetagenome#329 · Opened Sep 16, 2026
Consider contributing snpeff_build module to nf-core/modules Open

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

nf-core/viralmetagenome#328 · Opened Sep 16, 2026
Consider moving ivar_variants_to_vcf to nf-core/modules Open

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

nf-core/viralmetagenome#327 · Opened Sep 16, 2026
New pipeline: nf-core/genomeannotation Open

new-pipeline proposed

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

nf-core/proposals#169 · 2 comments · Opened Sep 15, 2026
metaT assemblies submisison Open

assembly_submit enhancement

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/seqsubmit#100 · Opened Sep 15, 2026
1.13.0: `--nf_core_pipeline mag` emits a samplesheet mag rejects (empty `group`, `fastq_1/2` instead of `short_reads_1/2`) Open

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

nf-core/fetchngs#401 · 1 reaction · Opened Sep 15, 2026
Minimac4 with unphased data Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/phaseimpute#311 · Opened Sep 15, 2026
Output reference phylogeny, alignment, taxonomy and model for phylogenetic placement Open

enhancement

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

nf-core/taxmarker#18 · 2 comments · Opened Sep 15, 2026
hap.py benchmarking silently produces empty results for GRCh37/b37 (non-chr-prefixed) references Open

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

nf-core/variantbenchmarking#324 · 1 comment · Opened Sep 15, 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
Csv samplesheet with only one individual Open

bug

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

nf-core/phaseimpute#310 · 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
Suitable for targeted data? Open

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

nf-core/pacsomatic#6 · Opened Sep 15, 2026
new module: metaproviz/internalstandard Open

new module

Difficulty 4/5 3-5 days Newbie friendliness 55/100

nf-core/modules#12957 · 1 comment · Opened Sep 15, 2026
new module: PSAURON Open

new module

nf-core/modules#12956 · 1 assignee · Opened Sep 14, 2026
Migrate to topic: universc Open

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

nf-core/modules#12951 · Opened Sep 14, 2026
Migrate to topic: narfmap/hashtable Open

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

nf-core/modules#12944 · Opened Sep 14, 2026
Migrate to topic: multiqc Open

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

nf-core/modules#12943 · 1 comment · Opened Sep 14, 2026
Migrate to topic: multiqcsav Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

nf-core/modules#12942 · 1 comment · Opened Sep 14, 2026
Optionally install/cache Nextflow plugins declared in nextflow.config Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/setup-nextflow#255 · Opened Sep 14, 2026

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