Skill: Download GDC

Use When

• A user wants to download BAM, VCF, FASTQ, or other files from the NCI GDC (TCGA, TARGET, CPTAC, etc.).
• A user has a GDC manifest file and wants to download all listed files.
• A user wants to query the GDC API to build a manifest by project, data type, workflow, or data category.
• A user wants to download controlled-access data using a GDC user token.
• A user wants to verify downloaded file integrity using MD5 checksums from the GDC manifest.
• A user wants to organize downloaded files by case, sample, or data type.

Inputs

• Required:
  • one of:
    • path to a GDC manifest file (TSV with columns: id, filename, md5, size, state)
    • GDC file UUID(s) to generate a manifest on the fly
    • GDC project ID (e.g., TCGA-BRCA) and filters to query and build a manifest
• Optional:
  • --token-file FILE — GDC user token for controlled-access data (required for dbGaP-protected files)
  • --outdir DIR — output directory (default: gdc_downloads)
  • --jobs N — number of parallel download streams (default: 1; max recommended: 8)
  • --retries N — retry count on network errors (default: 3)
  • --no-verify — skip MD5 verification after download
  • --dry-run — print manifest and download commands without executing
  • --data-type TYPE — filter for manifest generation (e.g., "Aligned Reads", "Masked Somatic Mutation")
  • --workflow TYPE — workflow filter (e.g., "STAR 2-Pass", "MuTect2")
  • --experimental-strategy — filter (e.g., "RNA-Seq", "WXS", "WGS")

Workflow

1. Obtain a manifest:
   • If a manifest file is provided, validate it (check columns: id, filename, md5, size, state).
   • If UUIDs are provided, generate a manifest via GDC API:

     curl -o manifest.txt \
       "https://api.gdc.cancer.gov/manifest?ids=$(echo "$UUIDS" | tr ' ' ',')"

   • If a project ID and filters are provided, query the GDC files endpoint and produce a manifest:

     curl -XPOST "https://api.gdc.cancer.gov/files" \
       -H "Content-Type: application/json" \
       -d '{"filters":{"op":"and","content":[
             {"op":"=","content":{"field":"cases.project.project_id","value":"TCGA-BRCA"}},
             {"op":"=","content":{"field":"data_type","value":"Aligned Reads"}},
             {"op":"=","content":{"field":"access","value":"open"}}]},
            "fields":"file_id,file_name,md5sum,file_size,state",
            "size":"10000","format":"tsv"}'

2. Check access tier: inspect the access field in the API response.
   • open: no token needed.
   • controlled: --token-file is required; warn the user if it is absent.
3. Download with gdc-client:

   gdc-client download \
     -m manifest.txt \
     [-t token.txt] \
     -d "$OUTDIR" \
     --n-processes "$JOBS" \
     --retry-amount "$RETRIES"

4. Verify MD5 checksums:

   while IFS=$'\t' read -r uuid filename md5 size state; do
     [[ "$uuid" == "id" ]] && continue
     actual=$(md5sum "$OUTDIR/$uuid/$filename" | awk '{print $1}')
     if [[ "$actual" != "$md5" ]]; then
       echo "CHECKSUM FAIL: $filename" >&2
     fi
   done < manifest.txt

5. Organize files (optional): flatten the <uuid>/<filename> layout into a user-specified directory structure by data type, project, or sample.
6. Write download_report.tsv with: uuid, filename, expected_md5, actual_md5, size_bytes, status.

Output Contract

• Downloaded files under <outdir>/<uuid>/<filename> (GDC default layout)
• manifest.txt used for the download (generated or provided)
• download_report.tsv with columns: uuid, filename, expected_md5, actual_md5, size_bytes, status (OK / CHECKSUM_FAIL / MISSING)
• failed_uuids.txt listing UUIDs that failed all retry attempts
• Exact gdc-client command issued

Limits

• GDC Data Transfer Tool (gdc-client) must be installed; download from https://gdc.cancer.gov/access-data/gdc-data-transfer-tool.
• Controlled-access data requires a GDC user token obtained from https://portal.gdc.cancer.gov after dbGaP authorization. Tokens expire after 30 days.
• Open-access files (e.g., gene expression counts, masked somatic mutations) do not require a token.
• GDC manifest files are project-snapshot–specific; file UUIDs are stable but a manifest generated today may differ from one generated later as projects update.
• Parallel downloads (--jobs > 1) may trigger GDC rate limiting; start with 3–4 jobs and increase cautiously.
• Common failure cases:
  • expired or invalid token causing 403 errors on controlled-access files
  • manifest containing files from multiple access tiers; download will fail on controlled-access files if no token is provided
  • disk space exhaustion for large TCGA BAM files (whole-genome BAMs are 50–200 GB each)
  • MD5 mismatch indicating a partial or corrupted download; delete the file and retry
  • mixing GDC file UUIDs with TCGA barcode IDs (barcodes must be resolved to UUIDs via the GDC API before use)