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
- name of metadata sample file
- liftoff_outputs (name configurable with
final_liftoff_output_dir)- name of metadata sample file
- errors
- fasta
- liftoff
- tbl
- name of metadata sample file
- 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
- name of annotation results (Liftoff or VADR, etc.)
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