SeqDB CLI Reference

The SeqDB CLI (seqdb) provides command-line access to the SeqDB platform for submitting genomic data, fetching reads, and integrating with nf-core pipelines.

Installation

pip install seqdb-cli

Authentication

# Login (stores credentials in ~/.seqdb/config.toml)
seqdb login --url https://api.seqdb.nfdp.dev --email you@example.com

# Logout
seqdb logout

Submitting Data

Download a template

seqdb template ERC000011 --output my_samples.tsv

Upload files to staging

seqdb upload reads/*.fastq.gz --threads 8

Validate a sample sheet

seqdb validate my_samples.tsv --checklist ERC000011

Submit (all-in-one)

Upload files, validate, and create entities in one command:

seqdb submit my_samples.tsv \
  --checklist ERC000011 \
  --project NFDP-PRJ-000001 \
  --files ./reads/ \
  --threads 8

Add --yes to skip the confirmation prompt.

Fetching Data

Fetch reads from SeqDB with nf-core-compatible samplesheet output:

# Fetch by project — downloads reads + generates samplesheet
seqdb fetch NFDP-PRJ-000001 -o ./data/

# Fetch by sample
seqdb fetch NFDP-SAM-000003 -o ./data/

# Generate presigned URLs instead of downloading
seqdb fetch NFDP-PRJ-000001 --urls-only -o ./data/

# Specify nf-core pipeline format
seqdb fetch NFDP-PRJ-000001 --format rnaseq -o ./data/
seqdb fetch NFDP-PRJ-000001 --format sarek -o ./data/

Using with nf-core pipelines

seqdb fetch NFDP-PRJ-000001 --format rnaseq -o ./data/
nextflow run nf-core/rnaseq --input ./data/samplesheet.csv

seqdb fetch NFDP-PRJ-000001 --format sarek -o ./data/
nextflow run nf-core/sarek --input ./data/samplesheet.csv

Supported formats

Format	Columns	Pipeline
generic	sample, fastq_1, fastq_2	Any
rnaseq	sample, fastq_1, fastq_2, strandedness	nf-core/rnaseq
sarek	patient, sample, lane, fastq_1, fastq_2	nf-core/sarek

Ingesting Results

Import MultiQC results back into SeqDB:

seqdb ingest NFDP-PRJ-000001 --multiqc ./results/multiqc_data/

Status & Search

# List recent projects
seqdb status

# Check a specific accession
seqdb status NFDP-PRJ-000001
seqdb status NFDP-SUB-000012

# Search
seqdb search "Bos taurus"

Common Workflows

Full submission workflow

# 1. Login
seqdb login --url https://api.seqdb.nfdp.dev --email you@example.com

# 2. Get a template
seqdb template ERC000011 -o samples.tsv

# 3. Fill in samples.tsv with your metadata

# 4. Submit with files
seqdb submit samples.tsv -c ERC000011 -p NFDP-PRJ-000001 -f ./reads/

# 5. Check status
seqdb status NFDP-PRJ-000001

Fetch and analyse

# 1. Fetch reads with samplesheet
seqdb fetch NFDP-PRJ-000001 --format rnaseq -o ./analysis/

# 2. Run nf-core pipeline
nextflow run nf-core/rnaseq --input ./analysis/samplesheet.csv

# 3. Ingest QC results back
seqdb ingest NFDP-PRJ-000001 --multiqc ./analysis/results/multiqc_data/

Options

All commands support --help for detailed usage:

seqdb --help
seqdb submit --help
seqdb fetch --help