IGF-HPC-Airflow/airflow_var/var.json

{
  "redis_conn_file":"/rds/general/user/igf/home/data2/airflow_test/secrets/redis_conn.json",
  "hpc_host":"login.hpc.ic.ac.uk",
  "hpc_user":"igf",
  "igf_lims_ssh_key_file":"/SSH/id_rsa",
  "hpc_ssh_key_file":"/home/igf/.ssh/id_rsa",
  "hpc_max_workers_per_queue":2,
  "hpc_max_total_workers":20,
  "seqrun_base_path":"",
  "seqrun_server_user":"",
  "database_config_file":"",
  "test_database_config_file":"",
  "slack_conf":"",
  "analysis_slack_conf":"",
  "asana_conf":"",
  "asana_demult_project":"",
  "asana_analysis_project":"",
  "ms_teams_conf":"",
  "analysis_ms_teams_conf":"",
  "hpc_seqrun_path":"",
  "box_dir_prefix_for_seqrun_report":"",
  "box_username":"",
  "box_config_file":"",
  "bcl2fastq_image_path":"",
  "interop_dumptext_exe":"",
  "interop_notebook_image_path":"",
  "seqrun_ml_notebook_template":"",
  "seqrun_training_data_csv":"",
  "interop_notebook_template":"",
  "pandoc_image_path":"",
  "singlecell_barcode_json":"",
  "singlecell_dual_barcode_json":"",
  "samplesheet_validation_json":"",
  "seqrun_server":"orwell.hh.med.ic.ac.uk",
  "orwell_server_hostname":"orwell.hh.med.ic.ac.uk",
  "woolf_server_hostname":"woolf.med.ic.ac.uk",
  "eliot_server_hostname":"eliot.med.ic.ac.uk",
  "igf_lims_server_hostname":"igf-lims.cc.ic.ac.uk",
  "tenx_single_cell_immune_profiling_feature_types": {"gene_expression":"","vdj-t":"","vdj-b":"","antibody_capture":"","antigen_capture":"","crisper_guide_capture":""},
  "scanpy_single_sample_template":"",
  "scvelo_single_sample_template": "",
  "scanpy_notebook_image":"",
  "scirpy_single_sample_template":"",
  "scirpy_notebook_image":"",
  "seurat_single_sample_template":"",
  "seurat_notebook_image":"",
  "irods_exe_dir":"",
  "ftp_hostname":"eliot.med.ic.ac.uk",
  "ftp_username":"igf",
  "ftp_project_path":"",
  "all_cell_marker_list":"",
  "cellranger_exe":"",
  "cellranger_job_timeout":259200,
  "cutadapt_singularity_image":"",
  "multiqc_singularity_image":"",
  "multiqc_template_file":"",
  "picard_singularity_image":"",
  "samtools_singularity_image":"",
  "igenome_base_path":"",
  "nextflow_template_file":"",
  "nextflow_exe":"",
  "nextflow_singularity_cache_dir":"",
  "seqrun_demult_notebook_template":"",
  "hpc_queue_list":{
    "hpc_1G": {
      "pbs_resource":"-lselect=1:ncpus=1:mem=1gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G"},
    "hpc_1G4t":{
      "pbs_resource":"-lselect=1:ncpus=4:mem=1gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t"},
    "hpc_4G":{
      "pbs_resource":"-lselect=1:ncpus=1:mem=4gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_4G"},
    "hpc_4G_long":{
      "pbs_resource":"-lselect=1:ncpus=1:mem=4gb -lwalltime=12:00:00",
      "airflow_queue":"hpc_1G,hpc_4G,hpc_4G_long"},
    "hpc_4G48hr":{
      "pbs_resource":"-lselect=1:ncpus=1:mem=4gb -lwalltime=48:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G48hr"},
    "hpc_4G4t":{
      "pbs_resource":"-lselect=1:ncpus=4:mem=4gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t"},
    "hpc_4G8t":{
      "pbs_resource":"-lselect=1:ncpus=8:mem=4gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t"},
    "hpc_4G16t":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=4gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t"},
    "hpc_8G":{
      "pbs_resource":"-lselect=1:ncpus=1:mem=8gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_4G,hpc_8G"},
    "hpc_8G4t":{
      "pbs_resource":"-lselect=1:ncpus=4:mem=8gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_8G,hpc_8G4t"},
      "hpc_8G_long":{
        "pbs_resource":"-lselect=1:ncpus=1:mem=8gb -lwalltime=24:00:00",
        "airflow_queue":"hpc_1G,hpc_4G,hpc_8G,hpc_8G_long"},
    "hpc_8G8t":{
      "pbs_resource":"-lselect=1:ncpus=8:mem=8gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_8G,hpc_8G4t,hpc_8G8t"},
    "hpc_8G16t":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=8gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16t"},
    "hpc_16G_long":{
        "pbs_resource":"-lselect=1:ncpus=1:mem=16gb -lwalltime=24:00:00",
        "airflow_queue":"hpc_1G,hpc_4G,hpc_8G,hpc_16G_long"},
    "hpc_16G4t":{
      "pbs_resource":"-lselect=1:ncpus=4:mem=16gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_8G,hpc_8G4t,hpc_16G4t"},
    "hpc_16G8t":{
      "pbs_resource":"-lselect=1:ncpus=8:mem=16gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_16G4t,hpc_16G8t"},
    "hpc_16G16t":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=16gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t"},
    "hpc_32G16t":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=32gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16t"},
    "hpc_42G16t":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=42gb -lwalltime=06:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t"},
    "hpc_64G16t24hr":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=64gb -lwalltime=24:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t,hpc_64G16t24hr"},
    "hpc_64G16t72hr":{
      "pbs_resource":"-lselect=1:ncpus=16:mem=64gb -lwalltime=72:00:00",
      "airflow_queue":"hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t,hpc_64G16t24hr,hpc_64G16t72hr"}
   }
}