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 validation_outdir)
  • name of metadata sample file
    • errors
    • fasta
    • tsv_per_sample
• liftoff_outputs (name configurable with final_liftoff_outdir)
  • name of metadata sample file
    • errors
    • fasta
    • liftoff
    • tbl
• vadr_outputs (name configurable with vadr_outdir)
  • name of metadata sample file
  • errors
  • fasta
  • gffs
  • tbl
• bakta_outputs (name configurable with bakta_outdir)
  • name of metadata sample file
  • fasta
  • gff
  • tbl
• submission_outputs (name and path configurable with submission_outdir)
  • individual_sample_batch_folder
    • biosample
    • sra
    • genbank
    • log_file
• final_submission_outputs (name and path configurable with final_submission_outdir)
  • updated_metadata_Excel_file
  • submission_report_file

Understanding Pipeline Outputs:¶

The pipeline outputs include:

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