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Update README.md #83

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Expand Up @@ -60,6 +60,8 @@ Currently, consists of two annotation options:
* The liftoff workflow annotates input fasta-formatted genomes and produces accompanying gff and genbank tbl files. The input includes the reference genome fasta, reference gff and your multi-sample fasta and metadata in .xlsx format. The [Liftoff](https://github.com/agshumate/Liftoff) workflow was brought over and integrated from the Liftoff tool, responsible for accurately mapping annotations for assembled genomes.
* (2) VADR
* The VADR workflow annotates input fasta-formatted genomes and generates gff / tbl files. The inputs into this workflow are your multi-sample fasta, metadata in .xlsx format, and reference information for the pathogen genome which is included within this repository (found [here](https://github.com/CDCgov/tostadas/tree/master/vadr_files/mpxv-models)). VADR is an existing package that was integrated into the pipeline and you can find more information about this tool at the following link: [VADR Git Repo](https://github.com/ncbi/vadr).
* (3) Bakta
* The Bakta workflow annotates input fasta-formatted bacterial genomes & plasmids and generates gff / tbl files. The inputs into this workflow are single-sample fasta, metadata in .xlsx format, and a reference database used for annotation (found [here](https://zenodo.org/records/7669534)). Bakta is an existing bacterial annotation tool that was integrated into the pipeline. You can find more information about this tool at the following link: [Bakta Git Repo](https://github.com/CDCgov/tostadas/tree/master#gene-annotation).

### Submission
Submission workflow generates the necessary files for Genbank submission, generates a BioSample ID, then optionally uploads Fastq files via FTP to SRA. This workflow was adapted from [SeqSender](https://github.com/CDCgov/seqsender) public database submission pipeline.
Expand Down Expand Up @@ -254,6 +256,7 @@ This section walks through the available parameters to customize your workflow.
| metadata | .xlsx | Multi-sample metadata matching metadata spreadsheets provided in input_files |
| ref_fasta | .fasta | Reference genome to use for the liftoff_submission branch of the pipeline |
| ref_gff | .gff | Reference GFF3 file to use for the liftoff_submission branch of the pipeline |
| db | folder | Bakta reference database used for bakta annotation |

#### (B) This table lists the required files to run with submission:
| Input files | File type | Description |
Expand Down Expand Up @@ -298,6 +301,7 @@ Table of entrypoints available for the nextflow pipeline:
| only_validation | Runs the metadata validation process only |
| only_liftoff | Runs the liftoff annotation process only |
| only_vadr | Runs the VADR annotation process only |
| only_bakta | Runs the Bakta annotation process only |
| only_submission | Runs submission sub-workflow only. Requires specific inputs mentioned here: [Required Files for Submission Entrypoint](#required-files-for-submission-entrypoint) |
| only_initial_submission | Runs the initial submission process but not follow-up within the submission sub-workflow. Requires specific inputs mentioned here: [Required Files for Submission Entrypoint](#required-files-for-submission-entrypoint) |
| only_update_submission | Updates NCBI submissions. Requires specific inputs mentioned here: [Required Files for Submission Entrypoint](#required-files-for-submission-entrypoint) |
Expand Down Expand Up @@ -371,6 +375,11 @@ The outputs are recorded in the directory specified within the nextflow.config f
* 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
Expand Down Expand Up @@ -405,21 +414,24 @@ When changing these parameters pay attention to the required inputs and make sur
| --ref_fasta_path | Reference Sequence file path | Yes (path as string) |
| --meta_path | Meta-data file path for samples | Yes (path as string) |
| --ref_gff_path | Reference gff file path for annotation | Yes (path as string) |
| --env_yml | Path to environment.yml file | Yes (path as string) |
| --db_path | Path to Bakta reference database | Yes (path as string) |
| --env_yml | Path to environment.yml file | Yes (path as string) |

### Run Environment
| Param | Description | Input Required |
|--------------------------|---------------------------------------------------------|------------------|
| --scicomp | Flag for whether running on Scicomp or not | Yes (true/false as bool) |
| --docker_container | Name of the Docker container | Yes, if running with docker profile (name as string) |
| --docker_container_vadr | Name of the Docker container to run VADR annotation | Yes, if running with docker profile (name as string) |
| --docker_container_bakta | Name of the Docker container to run Bakta annotation | Yes, if running with docker profile (name as string) |

### General Subworkflow
| Param | Description | Input Required |
|--------------------------|---------------------------------------------------------|------------------|
| --run_submission | Toggle for running submission | Yes (true/false as bool) |
| --run_liftoff | Toggle for running liftoff annotation | Yes (true/false as bool) |
| --run_vadr | Toggle for running vadr annotation | Yes (true/false as bool) |
| --run_bakta | Toggle for running Bakta annotation | Yes (true/false as bool) |
| --cleanup | Toggle for running cleanup subworkflows | Yes (true/false as bool) |

### Cleanup Subworkflow
Expand Down Expand Up @@ -474,6 +486,20 @@ When changing these parameters pay attention to the required inputs and make sur
| --vadr_output_dir | File path to vadr specific sub-workflow outputs | Yes (folder name as string) |
| --vadr_models_dir | File path to models for MPXV used by VADR annotation | Yes (folder name as string) |

### Bakta
| Param | Description | Input Required |
|-----------------------------|---------------------------------------------------------|------------------|
| --bakta_output_dir | File path to bakta specific sub-workflow outputs | Yes (folder name as string) |
| --bakta_min_contig_length | Minimum contig size | Yes (integer) |
| --bakta_threads | Number of threads to use while running annotation | Yes (integer) |
| --bakta_genus | Organism genus name | Yes (N/A or name as string) |
| --bakta_species | Organism species name | Yes (N/A or name as string) |
| --bakta_strain | Organism strain name | Yes (N/A or name as string) |
| --bakta_plasmid | Name of plasmid | Yes (unnamed or name as string) |
| --bakta_locus | Locus prefix | Yes (contig or name as string) |
| --bakta_locus_tag | Locus tag prefix | Yes (autogenerated or name as string) |
| --bakta_translation_table | Translation table | Yes (integer) |

### Sample Submission
| Param | Description | Input Required |
|--------------------------|---------------------------------------------------------|------------------|
Expand Down Expand Up @@ -501,6 +527,8 @@ When changing these parameters pay attention to the required inputs and make sur
:link: Liftoff Documentation: https://github.com/agshumate/Liftoff

:link: VADR Documentation: https://github.com/ncbi/vadr.git

:link: Bakta Documentation: https://github.com/oschwengers/bakta

:link: table2asn Documentation: https://github.com/svn2github/NCBI_toolkit/blob/master/src/app/table2asn/table2asn.cpp

Expand Down Expand Up @@ -533,7 +561,7 @@ When changing these parameters pay attention to the required inputs and make sur
Michael Desch | Ethan Hetrick | Nick Johnson | Kristen Knipe | Shatavia Morrison\
Yuanyuan Wang | Michael Weigand | Dhwani Batra | Jason Caravas | Ankush Gupta\
Kyle O'Connell | Yesh Kulasekarapandian | Cole Tindall | Lynsey Kovar | Hunter Seabolt\
Crystal Gigante | Christina Hutson | Brent Jenkins | Yu Li | Ana Litvintseva\
Crystal Gigante | Christina Hutson | Brent Jenkins | Yu Li | Ana Litvintseva | Swarnali Louha\
Matt Mauldin | Dakota Howard | Ben Rambo-Martin | James Heuser | Justin Lee | Mili Sheth


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