Long-Read-Proteogenomics-Workflow

What's Changed

• add metamorpheus by @rmillikin in #3
• visual studio stuff for metamorpheus by @rmillikin in #4
• append visual studio stuff to gitignore by @rmillikin in #5
• edit gitignore to not ignore C# app manifest by @rmillikin in #17
• [WIP] MetaMorpheus - take in ORF table info, use for protein inference by @rmillikin in #28
• Protein inference w rm kp by @gsheynkman in #35
• Dev by @bj8th in #103
• Another PR to Main - add additional modules by @gsheynkman in #105
• Removed DatabaseAnnoation. It is redundant with AccessionMapping module. by @gsheynkman in #106
• nextflow added to 6 frame by @bj8th in #107
• orf calling nextflowified - TransDecoder separated by @bj8th in #108
• updated code to have main. added nextflow to pg_gencodedb and pg_make… by @bj8th in #109
• Rmmiller rescue and resolve by @rmmiller22 in #113
• Updates command for SQANTI3 by @cgpu in #121
• Rmmiller rescue and resolve by @rmmiller22 in #115
• Updates ccs bam in run command for LR_IsoSeq3 by @cgpu in #118
• Bj8th nextflow by @bj8th in #125
• Adds accmapping module final code by @gsheynkman in #128
• Gloria dev by @gsheynkman in #130
• Adds accession mapping and protein group compare code by @gsheynkman in #131
• Enables use of 1 param runs with --config by @cgpu in #132
• Patch to enable large file deletion from git history by @cgpu in #135
• Bj8th protein db by @bj8th in #136
• Went over Ben's pipeline, Gloria added minor edits. by @bj8th in #137
• Nextflow edits gloria may22 by @gsheynkman in #138
• Scripts to download from AWS and upload to Zenodo, documentation regarding the process in AWStoZenodo.md. by @adeslatt in #140
• Bj8th by @bj8th in #145
• Delete branch.yml by @cgpu in #148
• Docs by @bj8th in #149
• This creates the accounting for running from Zenodo dealing with the two folders mass_spec and star_genome by @adeslatt in #143
• Adeslatt updates zenodo by @cgpu in #152
• Minor refactor of --metamorpheus_toml [debugs cloud execution] by @cgpu in #150
• Adds CI trigger for push to important branches [main, dev] by @cgpu in #154

Full Changelog: https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commits/v1.0.0