Outputs

Pipeline Overview:

The workflow will generate outputs in the following order:

• Validation
  • Responsible for QC of metadata
  • Aligns sample metadata .xlsx to sample .fasta
  • Formats metadata into .tsv format
• Annotation
  • Extracts features from .gff
  • Aligns features
  • Annotates sample genomes outputting .gff
• Submission
  • Formats for database submission
  • This section runs twice, with the second run occurring after a wait time to allow for all samples to be uploaded to NCBI.

Output Directory Formatting:

The outputs are recorded in the directory specified within the nextflow.config file and will contain the following:

• validation_outputs (name configurable with val_output_dir)
  • name of metadata sample file
    • errors
    • fasta
    • tsv_per_sample
• liftoff_outputs (name configurable with final_liftoff_output_dir)
  • name of metadata sample file
    • errors
    • fasta
    • liftoff
    • tbl
• vadr_outputs (name configurable with vadr_output_dir)
  • name of metadata sample file
    • errors
    • fasta
    • gffs
    • tbl
• bakta_outputs (name configurable with bakta_output_dir)
  • name of metadata sample file
    • fasta
    • gff
    • tbl
• submission_outputs (name and path configurable with submission_output_dir)
  • name of annotation results (Liftoff or VADR, etc.)
    • individual_sample_batch_info
      • biosample_sra
      • genbank
      • accessions.csv
    • terminal_outputs
    • commands_used

Understanding Pipeline Outputs:

The pipeline outputs include:

• metadata.tsv files for each sample
• separate fasta files for each sample
• separate gff files for each sample
• separate tbl files containing feature information for each sample
• submission log file
  • This output is found in the submission_outputs file in your specified output_directory