Allows NGSpeciesID w/Haplotype Phasing solo

Updated to allow for running FunDiS_NGSpeciesID.py on its own with Haplotype Phasing as an option.

Bug Fix - HS Round 2

Updated FunDiS_Minbar.py name, Corrected run_medaka.sh to properly init and handle conda environment calls, Corrected logging in GUI even if file isn't 'selected', i.e. it is pasted into the cell, Corrected medaka search to be in main Gui

Bug Fix - HS

Fixed searching for minibar.py appropriately and linked Reads in Consensus (RiC) cutoff being based on Summary value in GUI.

Sanity Check Release

Uploaded all files not included in previous release (Icons, Images, Shell Scripts, etc.)

Full Pipeline, QC, & Phasing Update

Built out the Graphical User Interface and established each part of the pipeline as a button to be run individually or as a whole pipeline. Also updated the setup shell script to aid in ensuring there is an environments available with all necessary requirements. This update does use the Phased Haplotype .fasta file in MycoMap summarizing, it can however, still use the default features developed by Stephen Douglas Russell. A Quality Control feature: Nanofilt via Chopper is implemented to ensure reads going through the pipeline are of specific quality and length. The main menu has also been updated to include space for variable command options for Chopper, Minibar, and NGSpeciesID.

Working GUI

Built out the Graphical User Interface and established each part of the pipeline as a button to be run individually. Also implemented a setup shell script to aid in ensuring there is an environments available with all necessary requirements to run both the main pipeline and medaka. NOTE: This currently does not use a Phased Haplotype FASTA file in MycoMap summarizing, it uses the default features developed by Stephen Douglas Russell. Utilization of the Phased Haplotype FASTA will come out in the next release.

Internal working pipeline

This is the final release of the full working pipeline on my internal system.

Refactored fundis_summarize.py & minor argument additions

Completely refactored summarizing and furthermore added arguments to make sure all parts of the pipeline are given the correct arguments.

Initial Commit

Initial commit of original version.