Miniwdl - Kincekara/C-BIRD GitHub Wiki

Inputs

Please check optional and required input definitions from the Terra page. JSON templates for C-BIRD and MultiBIRD inputs are given below.

JSON for all inputs of C-BIRD

{
  "cbird_workflow.read1": "/path/to/first/fastq/file",
  "cbird_workflow.read2": "/path/to/second/fastq/file",
  "cbird_workflow.samplename": "sample_name",
  "cbird_workflow.adapters": "/path/to/adapters/file",
  "cbird_workflow.kraken2_db": "/path/to/kraken2/database",
  "cbird_workflow.mash_reference": "/path/to/mash/reference",
  "cbird_workflow.checkm2_db": "/path/to/checkm2/database",
  "cbird_workflow.target_genes_fasta": "/path/to/target/genes/fasta",
  "cbird_workflow.minimum_total_reads": 30000,
  "cbird_workflow.labid": "lab_id",
  "cbird_workflow.report_logo1": "/path/to/report/logo1",
  "cbird_workflow.report_logo2": "/path/to/report/logo2",
  "cbird_workflow.report_disclaimer": "/path/to/report/disclaimer",
  "cbird_workflow.header_line1": "Header Line 1",
  "cbird_workflow.header_line2": "Header Line 2",
  "cbird_workflow.header_line3": "Header Line 3",
  "cbird_workflow.header_line4": "Header Line 4",
  "cbird_workflow.header_line5": "Header Line 5",
  "cbird_workflow.header_line6": "Header Line 6"
}

JSON for all inputs of multiBIRD

{
  "multibird.inputSamplesFile": "/path/to/samples.tsv",
  "multibird.adapters": "/path/to/adapters/file",
  "multibird.kraken2_db": "/path/to/kraken2/database",
  "multibird.mash_reference": "/path/to/mash/reference",
  "multibird.checkm2_db": "/path/to/checkm2/database",
  "multibird.target_genes_fasta": "/path/to/target/genes/fasta",
  "multibird.minimum_total_reads": 30000,
  "multibird.labid": "lab_id",
  "multibird.report_logo1": "/path/to/report/logo1",
  "multibird.report_logo2": "/path/to/report/logo2",
  "multibird.report_disclaimer": "/path/to/report/disclaimer",
  "multibird.header_line1": "Header Line 1",
  "multibird.header_line2": "Header Line 2",
  "multibird.header_line3": "Header Line 3",
  "multibird.header_line4": "Header Line 4",
  "multibird.header_line5": "Header Line 5",
  "multibird.header_line6": "Header Line 6"
}