sheynkman-lab/Long-Read-Proteogenomics: Long-Read-Proteogenomics-Workflow

What's Changed add metamorpheus by @rmillikin in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/3 visual studio stuff for metamorpheus by @rmillikin in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/4 append visual studio stuff to gitignore by @rmillikin in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/5 edit gitignore to not ignore C# app manifest by @rmillikin in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/17 [WIP] MetaMorpheus - take in ORF table info, use for protein inference by @rmillikin in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/28 Protein inference w rm kp by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/35 Dev by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/103 Another PR to Main - add additional modules by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/105 Removed DatabaseAnnoation. It is redundant with AccessionMapping module. by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/106 nextflow added to 6 frame by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/107 orf calling nextflowified - TransDecoder separated by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/108 updated code to have main. added nextflow to pg_gencodedb and pg_make… by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/109 Rmmiller rescue and resolve by @rmmiller22 in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/113 Updates command for SQANTI3 by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/121 Rmmiller rescue and resolve by @rmmiller22 in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/115 Updates ccs bam in run command for LR_IsoSeq3 by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/118 Bj8th nextflow by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/125 Adds accmapping module final code by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/128 Gloria dev by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/130 Adds accession mapping and protein group compare code by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/131 Enables use of 1 param runs with --config by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/132 Patch to enable large file deletion from git history by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/135 Bj8th protein db by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/136 Went over Ben's pipeline, Gloria added minor edits. by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/137 Nextflow edits gloria may22 by @gsheynkman in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/138 Scripts to download from AWS and upload to Zenodo, documentation regarding the process in AWStoZenodo.md. by @adeslatt in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/140 Bj8th by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/145 Delete branch.yml by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/148 Docs by @bj8th in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/149 This creates the accounting for running from Zenodo dealing with the two folders mass_spec and star_genome by @adeslatt in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/143 Adeslatt updates zenodo by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/152 Minor refactor of --metamorpheus_toml [debugs cloud execution] by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/150 Adds CI trigger for push to important branches [main, dev] by @cgpu in https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/154 Full Changelog: https://github.com/sheynkman-lab/Long-Read-Proteogenomics/commits/v1.0.