Data & utilitieslatest-release

seqsubmit

nf-core/seqsubmit

Submit sequences, assemblies, MAGs, etc., to public archives

version1.0.0717fd19e7aJul 31, 2026 Upstream Usage docs

Key tools

MultiQCCoverMCheckM2CAT and BATtRNAscan-SE 2.0barrnapENA Webin-CLIassembly_uploadergenome_uploader

Parameters

Groups

nf-core modules

Samplesheet cols

Run it

nfclaw

nfclaw run seqsubmit --input <input> --outdir results --centre-name <centre_name> --mode <mode> -profile docker

raw nextflow

nextflow run pipelines/seqsubmit/upstream -profile docker --input <input> --outdir results --centre_name <centre_name> --mode <mode>

demo · bundled test profile

nfclaw run seqsubmit --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

This release publishes no samplesheet schema for --input, so nfclaw does not pre-check its contents. The parameter reads: Path to samplesheet describing the data to be submitted (supported formats: csv, tsv, yaml, yml, json). Columns/fields depend on the pipeline mode. Configure the other inputs via parameters (see reference.md).

Secrets

This release reads Nextflow secrets: ENA_WEBIN (in nextflow.config, modules/local/registerstudy/main.nf); ENA_WEBIN_PASSWORD (in nextflow.config, modules/local/registerstudy/main.nf). Set each one a run needs with nextflow secrets set NAME VALUE before launching; a secret that is not set reaches its tasks as an empty value (Nextflow warns that the variable evaluates to an empty value), and a task that needs it then fails. Secrets are not written to nfclaw's provenance.

Resources

Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:

bash

nfclaw run seqsubmit --input <input> --outdir results --centre-name <centre_name> --mode <mode> -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.

Nextflow engine

This release declares nextflowVersion = '!>=25.10.4'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

bash

nfclaw run seqsubmit ... --nxf-ver 25.10.4

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Demo

bash

nfclaw run seqsubmit --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Required parameters

--inputstring (file path)

Path to samplesheet describing the data to be submitted (supported formats: csv, tsv, yaml, yml, json). Columns/fields depend on the pipeline mode

Constraint · matches ^\S+\.(csv|tsv|yaml|yml|json)$

--outdirstring (directory path)

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

--centre-namestring

Name of the submitter's organisation (mandatory for broker accounts).

--modestring

Type of the data to be submitted

magsbinsmetagenomic_assembliesreads

Parameter explorer

39 parameters · 7 groups

Every parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.

Groups

nextflow_schema.json

22 parameters · 17 hidden

Generic options4

Display the help message.

Display the full detailed help message.

Custom MultiQC yaml file containing HTML including a methods description.

Display hidden parameters in the help message (only works when --help or --help_full are provided).

Genome Evaluation options2

Path to pre-downloaded CheckM2 database. If omitted, downloads the version set by --checkm2_db_download_id

Zenodo ID for CheckM2 database download

Input Output options4

Email address for completion summary.

Path to samplesheet describing the data to be submitted (supported formats: csv, tsv, yaml, yml, json). Columns/fields depend on the pipeline mode

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Pipeline options9

Name of the submitter's organisation (mandatory for broker accounts).

Use that flag if you are referencing private data accessions in the samplesheet

Type of the data to be submitted

Date (YYYY-MM-DD) until which the newly created study stays private in ENA.

Path to a file (JSON, CSV, or TSV) with metadata for registering a new ENA study. Required if --submission_study is not set.

ENA study accession (PRJ/ERP) to submit the data to

Upload to ENA TEST server instead of LIVE server

Mark the assemblies as a Third PArty (TPA)

Webin-CLI mode for ENA interaction: submit uploads data, validate performs validation only.

Rna Detection options2

Minimum percentage of 16S, 23S, and 5S rRNA gene length recovered to count the gene as present.

Minimum number of tRNA genes detected to count tRNA as present. This value is defined by the MISAG/MIMAG standard and must not be modified.

Taxonomy Assignment options1

Path to local CAT_pack DB

Outputs

Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh. The exact output files and directory layout for this release are documented upstream: github.com/nf-core/seqsubmit/blob/1.0.0/docs/output.md Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.