Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cdcgov/tostadas issues and pull requests

#220 - [Internal] [Feature] Fix tests (for Github Actions)

Issue - State: open - Opened by jessicarowell 8 days ago
Labels: enhancement

#218 - Rewrites the submission module and fixes a lot of bugs

Pull Request - State: closed - Opened by jessicarowell 9 days ago

#215 - Seqsender rewrite ick4 2

Pull Request - State: closed - Opened by RamiyapriyaS 10 days ago

#215 - Seqsender rewrite ick4 2

Pull Request - State: closed - Opened by RamiyapriyaS 10 days ago

#214 - [Internal] [Bug] GenBank folder not showing up in outdir/submission_outputs

Issue - State: closed - Opened by jessicarowell 14 days ago - 1 comment
Labels: bug

#213 - [Internal] [Feature] Refactor to bulk-submit samples

Issue - State: open - Opened by jessicarowell 14 days ago
Labels: enhancement

#211 - [Internal] [Feature] Write a new update_submission.py script

Issue - State: open - Opened by jessicarowell 15 days ago
Labels: enhancement

#209 - [Internal] [Feature] Change name of fastq files before SRA upload

Issue - State: closed - Opened by jessicarowell 16 days ago - 1 comment
Labels: enhancement

#208 - Seqsender rewrite ick4 2

Pull Request - State: closed - Opened by RamiyapriyaS 17 days ago

#207 - Seqsender rewrite ick4 2

Pull Request - State: closed - Opened by RamiyapriyaS about 1 month ago

#206 - [Internal] [Feature] SRA Publication Delay Release

Issue - State: closed - Opened by jessicarowell about 1 month ago - 1 comment
Labels: enhancement

#205 - [Internal] [Bug] New code not generating report.xml after submission

Issue - State: closed - Opened by jessicarowell about 2 months ago - 1 comment
Labels: bug

#204 - [Internal] [Feature] Cloud support for submissions

Issue - State: open - Opened by jessicarowell about 2 months ago
Labels: enhancement

#203 - [Internal] [Feature] Build submission process directly into pipeline

Issue - State: closed - Opened by jessicarowell about 2 months ago
Labels: enhancement

#202 - [External] [Bug] CWE-798 Security Vulnerability - Plain Text Password

Issue - State: open - Opened by thomasphung about 2 months ago
Labels: bug

#201 - [External] [Bug] test fails at validation step

Issue - State: open - Opened by ammaraziz 4 months ago
Labels: bug

#200 - Rsv vadr refactor kao

Pull Request - State: closed - Opened by jessicarowell 6 months ago

#199 - [External] [Feature] Clarify Conda Requirement

Issue - State: closed - Opened by garfinjm 7 months ago - 1 comment
Labels: enhancement

#198 - [Internal] [Feature] Make these custom field validations "smarter"

Issue - State: open - Opened by jessicarowell 7 months ago
Labels: enhancement

#197 - Submission fasta reroute ick4

Pull Request - State: closed - Opened by jessicarowell 8 months ago
Labels: bug

#196 - Patch concatgffs ick4

Pull Request - State: closed - Opened by jessicarowell 8 months ago

#196 - Patch concatgffs ick4

Pull Request - State: closed - Opened by jessicarowell 8 months ago

#194 - Test data variola update kao

Pull Request - State: closed - Opened by jessicarowell 8 months ago
Labels: bug

#194 - Test data variola update kao

Pull Request - State: closed - Opened by jessicarowell 8 months ago
Labels: bug

#193 - change container from seqsender to tostadas

Pull Request - State: closed - Opened by jessicarowell 8 months ago

#193 - change container from seqsender to tostadas

Pull Request - State: closed - Opened by jessicarowell 8 months ago

#192 - Fix null path error for submission

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#192 - Fix null path error for submission

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#191 - [Internal] [Bug] fasta_path cannot be empty (sra-only submissions)

Issue - State: closed - Opened by jessicarowell 8 months ago
Labels: bug

#190 - User provided annotations for genbank submission

Pull Request - State: closed - Opened by kyleoconnell 8 months ago - 1 comment

#190 - User provided annotations for genbank submission

Pull Request - State: closed - Opened by kyleoconnell 8 months ago - 1 comment

#188 - Update container ick4

Pull Request - State: closed - Opened by jessicarowell 8 months ago

#187 - Submission ch path kao

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#187 - Submission ch path kao

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#186 - fixed channel mixup and removed remnants of utility function

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#185 - removed utility signal and cleanup files

Pull Request - State: closed - Opened by kyleoconnell 8 months ago

#184 - Seqera suggestions

Pull Request - State: closed - Opened by robsyme 8 months ago

#184 - Seqera suggestions

Pull Request - State: closed - Opened by robsyme 8 months ago

#183 - [Internal] [Feature] Ensure metadata validation is checking all fields required for NCBI submission

Issue - State: closed - Opened by kyleoconnell 8 months ago - 1 comment
Labels: enhancement

#182 - Update README.md

Pull Request - State: closed - Opened by RamiyapriyaS 9 months ago

#182 - Update README.md

Pull Request - State: closed - Opened by RamiyapriyaS 9 months ago

#181 - [Internal] [Feature] Recode SeqSender to modify data validation

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#180 - Update README.md

Pull Request - State: closed - Opened by RamiyapriyaS 9 months ago

#180 - Update README.md

Pull Request - State: closed - Opened by RamiyapriyaS 9 months ago

#179 - Samplesheet check metadata ufp0

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#178 - Samplesheet check metadata ufp0

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#178 - Samplesheet check metadata ufp0

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#177 - Params and metadata fix ick4

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#177 - Params and metadata fix ick4

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#176 - [Internal] [Feature] Evaluate if we need Run_utility or not

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#176 - [Internal] [Feature] Evaluate if we need Run_utility or not

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#175 - Update modules .config

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#174 - Update README.md

Pull Request - State: closed - Opened by RamiyapriyaS 9 months ago

#173 - [Internal] [Bug] Won't accept any 'dots' in sample file names

Issue - State: open - Opened by jessicarowell 9 months ago
Labels: bug

#173 - [Internal] [Bug] Won't accept any 'dots' in sample file names

Issue - State: open - Opened by jessicarowell 9 months ago
Labels: bug

#172 - [Internal] [Feature] Refactor to support nanopore data

Issue - State: open - Opened by jessicarowell 9 months ago
Labels: enhancement

#172 - [Internal] [Feature] Refactor to support nanopore data

Issue - State: open - Opened by jessicarowell 9 months ago
Labels: enhancement

#171 - change the . to - in species ID, in multifasta and metadata

Pull Request - State: closed - Opened by jessicarowell 9 months ago
Labels: bug

#171 - change the . to - in species ID, in multifasta and metadata

Pull Request - State: closed - Opened by jessicarowell 9 months ago
Labels: bug

#170 - Add bakta missing ick4

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#170 - Add bakta missing ick4

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#169 - [Internal] [Feature] Evaluate if we need 'Check Files' Module.

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#169 - [Internal] [Feature] Evaluate if we need 'Check Files' Module.

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#168 - update test data

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#168 - update test data

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#167 - Seqsender update

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#167 - Seqsender update

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#166 - update staphb container yml file for new seqsender code

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#165 - Merging into Dev instead of Main.

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#164 - merge refactoring of bakta to a single subworkflow into dev

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#164 - merge refactoring of bakta to a single subworkflow into dev

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#163 - merge bakta module fixes into dev

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#163 - merge bakta module fixes into dev

Pull Request - State: closed - Opened by jessicarowell 9 months ago

#162 - 161 refactor bakta with extra params

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#162 - 161 refactor bakta with extra params

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#160 - [Internal] [Bug] **Installation for CDC**

Issue - State: closed - Opened by lskatz 9 months ago - 1 comment
Labels: bug

#160 - [Internal] [Bug] **Installation for CDC**

Issue - State: closed - Opened by lskatz 9 months ago - 1 comment
Labels: bug

#159 - Bakta Refresh

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#159 - Bakta Refresh

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#158 - [Internal] [Feature] Convert param validation to nf-core validation plugin

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#158 - [Internal] [Feature] Convert param validation to nf-core validation plugin

Issue - State: closed - Opened by kyleoconnell 9 months ago - 1 comment
Labels: enhancement

#157 - Add new test data kao

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#157 - Add new test data kao

Pull Request - State: closed - Opened by kyleoconnell 9 months ago

#156 - GitHub pages to master

Pull Request - State: closed - Opened by macoven-del 9 months ago - 1 comment

#156 - GitHub pages to master

Pull Request - State: closed - Opened by macoven-del 9 months ago - 1 comment

#155 - [Internal] [Feature] Move viral and bacterial annotation to subworkflows

Issue - State: closed - Opened by kyleoconnell 10 months ago
Labels: enhancement

#155 - [Internal] [Feature] Move viral and bacterial annotation to subworkflows

Issue - State: closed - Opened by kyleoconnell 10 months ago
Labels: enhancement

#154 - [Internal] [Feature] Check metadata date format

Issue - State: closed - Opened by kyleoconnell 10 months ago - 1 comment
Labels: enhancement

#153 - Dev

Pull Request - State: closed - Opened by kyleoconnell 10 months ago

#153 - Dev

Pull Request - State: closed - Opened by kyleoconnell 10 months ago