prefix,assembly,taxid
BU_ATCC8492VPI0062,/path/to/BU_ATCC8492VPI0062_NT5002.fa,820
EC_ASM584v2,/path/to/GCF_000005845.2.fna,562
...

python3 preprocessing/generate_input_file.py -h
usage: generate_input_file.py [-h] -i INFILE -d INPUT_DIR -b BAT_DIR -o OUTFILE [--no-prefix]

The script takes a list of genomes and the taxonomy results generated by BAT and makes a
mettannotator input csv file. The user has the option to either use the genome file name
(minus the extension) as the prefix for mettannotator or leave the prefix off and fill it
out themselves after the script generates an input file with just the FASTA location and
the taxid. It is expected that for all genomes, BAT results are stored in the same folder
and are named as {fasta_base_name}.bin2classification.txt. The script will use the lowest-
level taxid without an asterisk as the taxid for the genome.

optional arguments:
  -h, --help    show this help message and exit
  -i INFILE     A file containing a list of genome files to include (file name only, with file
                extension, unzipped, one file per line).
  -d INPUT_DIR  Full path to the directory where the input FASTA files are located.
  -b BAT_DIR    Folder with BAT results. Results for all genomes should be in the same folder
                and should be named {fasta_base_name}.bin2classification.txt
  -o OUTFILE    Path to the file where the output will be saved to.
  --no-prefix   Skip prefix generation and leave the first column of the output file empty for
                the user to fill out. Default: False

nextflow run ebi-metagenomics/mettannotator/main.nf --help
N E X T F L O W  ~  version 23.04.3
Launching `mettannotator/main.nf` [disturbed_davinci] DSL2 - revision: f2a0e51af6


------------------------------------------------------
  ebi-metagenomics/mettannotator <version>
------------------------------------------------------
Typical pipeline command:

  nextflow run ebi-metagenomics/mettannotator --input assemblies_sheet.csv -profile docker

Input/output options
  --input                            [string]  Path to comma-separated file containing information about the assemblies with the prefix to be used.
  --outdir                           [string]  The output directory where the results will be saved. You have to use absolute paths to storage on Cloud
                                               infrastructure.
  --fast                             [boolean] Run the pipeline in fast mode. In this mode, InterProScan, UniFIRE, and SanntiS won't be executed, saving
                                               resources and speeding up the pipeline.
  --email                            [string]  Email address for completion summary.
  --multiqc_title                    [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference databases
  --dbs                              [string]  Folder for the tools' reference databases used by the pipeline for downloading.
  --interproscan_db                  [string]  The InterProScan reference database, ftp:https://ftp.ebi.ac.uk/pub/software/unix/iprscan/
  --interproscan_db_version          [string]  The InterProScan reference database version. [default: 5.62-94.0]
  --interpro_entry_list              [string]  TSV file listing basic InterPro entry information - the accessions, types and names,
                                               ftp:https://ftp.ebi.ac.uk/pub/databases/interpro/releases/94.0/entry.list
  --interpro_entry_list_version      [string]  InterPro entry list version [default: 94]
  --eggnog_db                        [string]  The EggNOG reference database folder,
                                               https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#requirements
  --eggnog_db_version                [string]  The EggNOG reference database version. [default: 5.0.2]
  --rfam_ncrna_models                [string]  Rfam ncRNA models, ftp:https://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/ncrna/
  --rfam_ncrna_models_rfam_version   [string]  Rfam release version where the models come from. [default: 14.9]
  --amrfinder_plus_db                [string]  AMRFinderPlus reference database,
                                               https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/. Go to the following
                                               documentation for the db setup https://github.com/ncbi/amr/wiki/Upgrading#database-updates.
  --amrfinder_plus_db_version        [string]  The AMRFinderPlus reference database version. [default: 2023-02-23.1]
  --defense_finder_db                [string]  Defense Finder reference models, https://github.com/mdmparis/defense-finder#updating-defensefinder. The
                                               Microbiome Informatics team provides a pre-indexed version of the models for version 1.2.3 on this ftp location:
                                               ftp:https://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/defense-finder/defense-finder-models_1.2.3.tar.gz.
  --defense_finder_db_version        [string]  The Defense Finder models version. [default: 1.2.3]
  --antismash_db                     [string]  antiSMASH reference database, go to this documentation to do the database setup
                                               https://docs.antismash.secondarymetabolites.org/install/#installing-the-latest-antismash-release.
  --antismash_db_version             [string]  The antiSMASH reference database version. [default: 7.1.0]
  --dbcan_db                         [string]  dbCAN indexed reference database, please go to the documentation for the setup
                                               https://dbcan.readthedocs.io/en/latest/. The Microbiome Informatics team provides a pre-indexed version of the
                                               database for version 4.0 on this ftp location:
                                               ftp:https://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/dbcan/dbcan_4.0.tar.gz
  --dbcan_db_version                 [string]  The dbCAN reference database version. [default: 4.1.3_V12]

Generic options
  --multiqc_methods_description      [string]  Custom MultiQC yaml file containing HTML including a methods description.

Other parameters
  --bakta                            [boolean] Use Bakta instead of Prokka for CDS annotation. Prokka will still be used for archaeal genomes.

 !! Hiding 17 params, use --validationShowHiddenParams to show them !!
------------------------------------------------------
If you use ebi-metagenomics/mettannotator for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/ebi-metagenomics/mettannotator/blob/master/CITATIONS.md
------------------------------------------------------

└─<PREFIX>
   ├─antimicrobial_resistance
   │  └─amrfinder_plus
   ├─antiphage_defense
   │  └─defense_finder
   ├─biosynthetic_gene_clusters
   │  ├─antismash
   │  ├─gecco
   │  └─sanntis
   ├─functional_annotation
   │  ├─dbcan
   │  ├─eggnog_mapper
   │  ├─interproscan
   │  ├─merged_gff
   │  ├─prokka
   │  └─unifire
   ├─mobilome
   │  └─crisprcas_finder
   ├─quast
   │  └─<PREFIX>
   │      ├─basic_stats
   │      └─icarus_viewers
   ├─rnas
   │  ├─ncrna
   │  └─trna
   ├─multiqc
   │  ├─multiqc_data
   │  └─multiqc_plots
   │      ├─pdf
   │      ├─png
   │      └─svg
   ├─pipeline_info
   │  ├─software_versions.yml
   │  ├─execution_report_<timestamp>.txt
   │  ├─execution_report_<timestamp>.html
   │  ├─execution_timeline_<timestamp>.txt
   │  ├─execution_timeline_<timestamp>.html
   │  ├─execution_trace_<timestamp>.txt
   │  ├─execution_trace_<timestamp>.html
   │  └─pipeline_dag_<timestamp>.html