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File Staging & Upload

Files must be staged (uploaded to a temporary area) before they can be linked to samples via bulk submission.

Upload methods

  1. Go to Submit → Bulk Submit → Step 2 (Upload Files)
  2. Click Choose Files to select one or more files
  3. Files upload directly to the backend
  4. MD5 checksums are computed server-side automatically
  5. Upload progress is shown per file

API upload

curl -X POST http://localhost:8000/api/v1/staging/upload \
  -H "Authorization: Bearer $TOKEN" \
  -F "file=@SAMPLE_001_R1.fastq.gz"

Response: 

{
  "id": 1,
  "filename": "SAMPLE_001_R1.fastq.gz",
  "file_size": 1234567890,
  "checksum_md5": "d41d8cd98f00b204e9800998ecf8427e",
  "status": "VERIFIED",
  "upload_method": "direct",
  "created_at": "2026-01-15T10:30:00"
}

For files larger than 5 GB, use FTP to avoid browser timeout issues.

Connect

# Using lftp (recommended — supports resume)
lftp -u your_email@example.com ftp://ftp.nfdp.example.sa
> mput *.fastq.gz
> quit

# Using standard ftp
ftp ftp.nfdp.example.sa
> put SAMPLE_001_R1.fastq.gz

# Using FileZilla
Host: ftp.nfdp.example.sa
Username: your_email@example.com
Password: your SeqDB password
Port: 21

Tips

  • Use lftp for resume support on interrupted uploads
  • Upload to your user directory — files appear in staging automatically
  • Supported formats: .fastq, .fastq.gz, .fq, .fq.gz, .bam, .cram, .vcf, .vcf.gz

Managing staged files

List staged files

curl -H "Authorization: Bearer $TOKEN" \
  http://localhost:8000/api/v1/staging/files

Delete a staged file

curl -X DELETE http://localhost:8000/api/v1/staging/files/42 \
  -H "Authorization: Bearer $TOKEN"

What happens to staged files

  1. Upload — File stored in staging bucket (nfdp-staging)
  2. Validation — Bulk submit matches staged files to sample sheet rows
  3. Confirmation — Matched files are linked to runs and marked as "linked"
  4. Cleanup — Linked files are moved from staging to the raw bucket (nfdp-raw)

Files persist across sessions

Staged files remain available until used or deleted. You can upload files in one session and submit the sample sheet later.