Ampcombi

-- Added a check if ./temp dir is found before removal. This caused problems with pipeline setups.

-- Fixed the package versions in setup
-- Adjusted readme for installation setup
-- Fixed the `./temp` dir removal step at the end of the process
-- Changed the default matrix in diamond blastp to PAM250

-- Change the output extension from `.csv` to `.tsv`
-- Added a new feature to estimate the isoelectric point, mwt, structure fraction and hydrophobicity
-- The DRAMP db `.tsv` was filtered to retain only necessary columns
-- Added the tool AMPtransformer
-- Added the tool AMPgram
-- Fixed hmmsearch to now parse both single and multi models
-- Fixed the dependencies in the environment.yml file
-- Added a log file for each sample, besides the main log for the complete summary. Beneficial when used in pipelines like nf-core/funcscan
-- Added the parameter '--sample_metadata' an optional flag to add a file with sample metadata
-- Added the parameter '--contig_metadata' an optional flag to add a file with contig metadata
-- Removed tooldictionary parameter '--tooldict' and added a parameter for each tool instead '--<tool>_file' to assign the extension of the files per tool
-- Added the parameter `--hmm_evalue` to filter the hmm results in the table based on E-value
-- Added the parameter `--aminoacid_length` to retain hits with a specific length
-- Added the parameter `--db_evalue` to filter out classification hits below specific diamond E-values
-- Renamed the parameter `--cutoff` to `--amp_cutoff`
-- Added the parameter '--gbk' to add gbk files as input for parsing to include contig ids and other important values
-- Added the parameter '--window_size_stop_codon' that adjusts the window size to look for stop codons
-- Added the parameter '--remove_stop_codons' that removes hits with no stop codons found in the vicinity
-- Added the parameter '--window_size_transporter' that adjusts the window size to look for 'transporter' proteins
-- Added a new output directory per sample that holds the gbk files for the contigs with hits
-- Added the submodule to cluster the AMP hits with the parameters to modify the clustering using [MMSeqs2](https://github.com/soedinglab/MMseqs2) for e.g., '--cluster_cov_mode' '--cluster_mode' '--cluster_coverage' '--cluster_seq_id' '--cluster_sensitivity' '--cluster_remove_singletons' '--cluster_retain_label' '--cluster_min_member'
-- Added the submodule to predict signaling peptide using [SignalP-6.0h](https://services.healthtech.dtu.dk/services/SignalP-6.0/)
-- Removed the HTML output for the complete summary and replaced it with shiny for python app that can be viewed using the commandline
-- Updated AMPcombi to use subcommands for ease of use with standardized and portable piplines

-- Linked to Zenodo archive

-- Included the possibility of only submitting one .faa file instead of the faa-folder path (in case of summarizing only one single sample)

-- Included the HTML output for the complete summary
-- add option --threads for diamond (make database and alignment)
-- included check if database was downloaded once to not download again