nf-core pipeline ·
nf-core/seqsubmit
Automates the submission of raw sequencing reads, metagenomic assemblies, MAGs, and bins to the ENA.
What nf-core/seqsubmit is
nf-core/seqsubmit is a bioinformatics pipeline for depositing sequencing data directly into the European Nucleotide Archive (ENA). It was created by Martin Beracochea, Ekaterina Sakharova, Sofia Ochkalova, and Tim Rozday, with development assistance from Evangelos Karatzas.
Submitting sequence data and metagenome-derived products to public databases involves stringent metadata requirements, file formatting conventions, and accession tracking. This pipeline streamlines deposition by providing standardised paths for uploading raw reads, contiguous assemblies, metagenome-assembled genomes (MAGs), and genomic bins.
What the pipeline does
The pipeline executes one of three underlying workflows determined by the chosen operating mode: READSUBMIT for raw read sets, ASSEMBLYSUBMIT for metagenomic contigs, or GENOMESUBMIT for metagenome-assembled genomes and bins. Users provide a mode-specific CSV samplesheet containing file locations alongside biological, technical, and environmental metadata, together with an existing study accession or study registration file.
User authentication is performed against the ENA Webin service using Nextflow secrets. The pipeline structures metadata manifests, links reference accessions, and submits data files to generate per-sample submission receipts, registered accessions, coverage tables, execution metrics, and a MultiQC report.
Key facts
- Pipeline Workflows
- READSUBMIT, ASSEMBLYSUBMIT, GENOMESUBMIT
- Supported Submission Modes
- reads, metagenomic_assemblies, mags, bins
- Destination Archive
- European Nucleotide Archive (ENA)
- Authentication Mechanism
- ENA Webin credentials stored in Nextflow secrets
- Nextflow Version Requirement
- >=25.04.0
- Latest Release
- 1.0.0 (2026-08-04)
What you can use it for
- Raw Read Archival
- Submitting raw FASTQ sequencing files to ENA using the READSUBMIT workflow with associated sequencing platform, library strategy, and sample accession metadata.
- Metagenomic Assembly Deposition
- Registering assembled metagenome FASTA files alongside run accessions, coverage figures, and assembler software details using the ASSEMBLYSUBMIT workflow.
- MAG and Bin Submission
- Submitting metagenome-assembled genomes or bin FASTA files through the GENOMESUBMIT workflow with CheckM2 quality metrics, NCBI taxonomy, and environmental descriptors.
Run it here
The research agent runs nf-core/seqsubmit with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Provides dedicated, purpose-built workflows tailored to raw reads, metagenomic assemblies, and genome bins.
- Stores Webin credentials safely away from run parameters via Nextflow secrets.
- Outputs structured submission receipts and official accessions alongside MultiQC logs and pipeline traces.
Watch out for
- Requires pre-existing ENA accessions for samples, runs, or assemblies depending on the submission mode.
- Requires an active ENA Webin account and pre-configured Nextflow secrets before execution.
- Requires Nextflow version 25.04.0 or later.
Questions
Can I run nf-core/seqsubmit without my own cluster?
The research agent runs nf-core/seqsubmit with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/seqsubmit under?
MIT, like every nf-core pipeline.
What submission modes are available?
The pipeline provides four modes: 'reads' via READSUBMIT, 'metagenomic_assemblies' via ASSEMBLYSUBMIT, and 'mags' or 'bins' via GENOMESUBMIT.
How are ENA Webin credentials passed to the pipeline?
Credentials must be configured as Nextflow secrets under the names ENA_WEBIN and ENA_WEBIN_PASSWORD.
What prerequisites must be registered before running the pipeline?
A study accession or study registration file is required, and depending on the mode, prerequisite sample, read, or assembly accessions must be obtained from ENA beforehand.
What files are output after a successful run?
Outputs include per-sample submission receipts, accession lists, assembly or genome metadata files, MultiQC summary reports, and execution pipeline metrics.
How to cite it
Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research. 2022;51(D1):D753-9. doi:10.1093/nar/gkac1080
Written from nf-core/seqsubmit's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.