Argo data submission packages

Workflow for interacting with EGA and download files off their servers using Pyega3 or Aspera.

Given a CSV file of:

1. Registered samples
2. EGA ids (minimum EGAFs)
3. metadata json payloads (Optional. If provided will verify elements otherwise will auto generate)

Run generate_params_json.py for nextflow params file specific to one sample:

python3 generate_params_json.py -o ${working_directory} -c ${input_csv} -s {sample_of_interest}

For output see example_config.json

To run as aspera

export ASCP_SCP_HOST=''
export ASCP_SCP_USER=''
export ASPERA_SCP_PASS=''
export C4GH_PASSPHRASE=''
export ICGC_ARGO_API_TOKEN=''

nextflow \\
argo-data-submission/main.nf \\
-params-file example.json \\
-profile aspera \\
--api_token ${ICGC_ARGO_API_TOKEN}

To run as pyega3

export PYEGA3_EGA_USER=""
export PYEGA3_EGA_PASS=""
export ICGC_ARGO_API_TOKEN=''

nextflow \\
argo-data-submission/main.nf \\
-params-file example.json \\
-profile pyega3 \\
--api_token ${ICGC_ARGO_API_TOKEN}