Darcy220606/AMPcombi: v.0.2.0

AMPcombi v.0.2.0: This update was done with extensive scientific advice from Dr. Rosa Herbst.

Changes made include:

• 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 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
• 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