# metadata.json file for metatranscriptome filtering
{
  "inputs": [ "<seq_unit_name>" ],
  "metadata": {
    "analysis_project_id" : [<analysis_project_id>],
    "analysis_task_id" : [<analysis_task_id>],
    "library_name": ["<library_name>"], 
    "sequencing_project_id": [<seq_project_id>], 
    "seq_unit_name" : ["<seq_unit_base_name>"],
    "filter_product_type" : "<filter_method>",
    "input_read_count": <input_read_count>,
    "input_base_count" : <input_base_count>,
    "filter_reads_count" : <filter_read_count>,
    "filter_base_count" : <filter_base_count>,
    "filter_reads_count_pct" : <filter_read_count_pct>,
    "filter_base_count_pct" : <filter_base_count_pct>,    
    "bbtools_version" : "<bbtools_version>",
    "filter_pipeline_version" : "<filter_pipeline_version>",
    "rqc_filter_command" : "<rqc_filter_command>"
  }, 
  "outputs": [
    {
      "file": "<filter_fastq_file>", 
      "label": "filtered_fastq",
      "metadata" : { "illumina_sdm_seq_unit_id" : <sdm_seq_unit_id>, "fastq_type" : "filtered" }
    }, 
    {
      "file": "<rrna_filter_fastq_file>", 
      "label": "rrna_filtered_fastq",
      "metadata" : { "illumina_sdm_seq_unit_id" : <sdm_seq_unit_id>, "fastq_type" : "rrna filtered" }
    },
    {
      "file": "<filter_chaff_fastq_file>", 
      "label": "filtered_reads_chaff",
      "metadata" : { "illumina_sdm_seq_unit_id" : <sdm_seq_unit_id> }
    },       
    {
      "file" : "<filter_txt_report>",
      "label" : "filtered_report"
    },
    {
      "file" : "<filter_txt_method>",
      "label" : "filtered_methods_report"
    },
    {
      "file" : "<filter_commands>",
      "label" : "filter_commands"
    },
    {
      "file" : "spikein.fq.gz",
      "label" : "metatranscriptome_spikein_fastq"
    },
    {
      "file" : "scaffoldStatsSpikein.txt",
      "label" : "scaffold_spikein_stats"
    }    
  ]
}
