Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / BU-ISCIII/relecov-tools issues and pull requests
#309 - Release v1.1.0
Pull Request -
State: closed - Opened by Shettland 6 days ago
#308 - Pre-release 1.1.0. Includes fixing github actions
Pull Request -
State: closed - Opened by Shettland 6 days ago
#307 - bioinfo_config.json documentation
Issue -
State: open - Opened by Shettland 7 days ago
Labels: documentation
#306 - Now read-bioinfo-metadata splits data and extract files for each batch
Pull Request -
State: closed - Opened by Shettland 7 days ago
- 1 comment
#305 - Merge pull request #298 from BU-ISCIII/develop
Pull Request -
State: closed - Opened by Shettland 7 days ago
#304 - fix minor bug launch pipeline for copying r2
Pull Request -
State: closed - Opened by saramonzon 10 days ago
#303 - Fixes and improvements in launch_pipeline
Pull Request -
State: closed - Opened by saramonzon 14 days ago
#302 - Create a wrapper that launches download, read-lab-metadata and validate
Issue -
State: open - Opened by Shettland 15 days ago
Labels: enhancement
#301 - Fix test_sftp_handle workflow concurrency issues
Issue -
State: open - Opened by Shettland 15 days ago
Labels: bug
#300 - log_summary creates an excel file from logs
Pull Request -
State: closed - Opened by Shettland 15 days ago
- 2 comments
#299 - Included pango-data version extraction in read-bioinfo-metadata
Pull Request -
State: closed - Opened by Shettland 15 days ago
- 2 comments
#298 - Release 1.0.0
Pull Request -
State: closed - Opened by Shettland 17 days ago
#297 - Add upload_database tests to github actions
Issue -
State: open - Opened by Shettland 17 days ago
Labels: enhancement
#296 - Pre-release changes for version 1.0.0
Pull Request -
State: closed - Opened by Shettland 20 days ago
#295 - upload database module updated
Pull Request -
State: closed - Opened by luissian 21 days ago
- 2 comments
#294 - Add Build Schema Test to GitHub Actions
Issue -
State: open - Opened by Daniel-VM 23 days ago
#293 - Lack of `--log-file` core functionality in module `build-schema`
Issue -
State: open - Opened by Daniel-VM 23 days ago
#292 - fixing bugs on pipeline manager
Pull Request -
State: closed - Opened by luissian 27 days ago
#291 - Include data_validation in template
Issue -
State: open - Opened by Shettland 27 days ago
Labels: enhancement
#290 - read-lab date parse hotfix
Pull Request -
State: closed - Opened by Shettland 28 days ago
#289 - Hotfix for invalid date check in read-lab-metadata
Pull Request -
State: closed - Opened by Shettland 29 days ago
#288 - Standardize output filenames
Pull Request -
State: closed - Opened by Shettland 29 days ago
#287 - Created new class SFTPRelecov for sftp functions
Pull Request -
State: closed - Opened by luissian about 1 month ago
#286 - issue 284. created new module for pipeline launch
Pull Request -
State: closed - Opened by luissian about 2 months ago
- 1 comment
#285 - Included full_update arg to update-db + schema and config changes
Pull Request -
State: closed - Opened by Shettland about 2 months ago
#284 - Create an option to create simbolic links to Analisys folder
Issue -
State: closed - Opened by luissian about 2 months ago
Labels: enhancement
#283 - Convert custom logs to xlsx format
Issue -
State: open - Opened by Shettland about 2 months ago
Labels: enhancement
#282 - Log_summary could output the generated custom log in a folder named "logs"
Issue -
State: open - Opened by Shettland about 2 months ago
Labels: enhancement
#281 - Updated log_summary.py with new path field and renamed keys
Pull Request -
State: closed - Opened by Shettland 2 months ago
#280 - Better sftp cleaning and download logging
Pull Request -
State: closed - Opened by Shettland 2 months ago
#279 - Validate module now creates a validated metadata json file
Pull Request -
State: closed - Opened by Shettland 2 months ago
#278 - Now json_summary custom log filename includes module called
Pull Request -
State: closed - Opened by Shettland 2 months ago
#277 - Fix regex pattern and update metadata handling in read-bioinfo-metadata module
Pull Request -
State: closed - Opened by Daniel-VM 2 months ago
#276 - Include a test for file integrity somewhere in the workflow
Issue -
State: open - Opened by Shettland 2 months ago
Labels: enhancement
#275 - Missing fields when read-bioinfo-metadata is executed
Issue -
State: closed - Opened by Shettland 2 months ago
Labels: bug
#274 - Create validated.json keeping only samples that passed validation process
Issue -
State: closed - Opened by Shettland 3 months ago
Labels: enhancement
#273 - New module `build_schema`
Pull Request -
State: closed - Opened by Daniel-VM 3 months ago
- 3 comments
#272 - Enhance json schema validation with custom validators
Pull Request -
State: open - Opened by Daniel-VM 3 months ago
- 1 comment
#271 - Enhance JSON Schema validation with custom validators for complex propertyIDs
Issue -
State: open - Opened by Daniel-VM 3 months ago
Labels: enhancement
#270 - test
Pull Request -
State: closed - Opened by saramonzon 4 months ago
#269 - Hotfix for tmp folder creation in remote home
Pull Request -
State: closed - Opened by Shettland 4 months ago
#268 - Automatically send email of process log summary to the lab
Issue -
State: open - Opened by Shettland 4 months ago
Labels: enhancement
#267 - Read-bioinfo-metadata creates output even with no matching samples
Issue -
State: open - Opened by Shettland 4 months ago
Labels: bug
#266 - Changing how analysis_date is collected from variants_long_table
Issue -
State: open - Opened by Shettland 4 months ago
Labels: enhancement
#265 - Fixed actions pull-requests error again
Pull Request -
State: closed - Opened by Shettland 4 months ago
#264 - Splitted tests in two files, fixed pull-request checkout error
Pull Request -
State: closed - Opened by Shettland 4 months ago
#263 - Changing all the enums in each schema to lowercase
Issue -
State: open - Opened by Shettland 4 months ago
#262 - Introduced log_summary module for custom logs. Improvements in read-lab and excel-merging in sftp_handle
Pull Request -
State: closed - Opened by Shettland 4 months ago
- 1 comment
#261 - Limited concurrency in tests, changed swabbing in schema and utils.read_excel()
Pull Request -
State: closed - Opened by Shettland 4 months ago
#260 - update read-bioinfo-metadata readme
Pull Request -
State: closed - Opened by Daniel-VM 5 months ago
#259 - Create new module to generate, update and track JSON schema versions
Issue -
State: closed - Opened by Daniel-VM 5 months ago
#258 - Refactor of read-bioinfo-metadata module for tool compatibility expansion
Pull Request -
State: closed - Opened by Daniel-VM 6 months ago
- 3 comments
#257 - Small fix of tests and blood included in anatomical material
Pull Request -
State: closed - Opened by Shettland 6 months ago
- 1 comment
#256 - New workflow to test modules and new testing dataset
Pull Request -
State: closed - Opened by Shettland 6 months ago
#255 - Improvements in download module, merging folders in sftp and log_summary implementation
Pull Request -
State: closed - Opened by Shettland 7 months ago
- 1 comment
#254 - Unique identifier for each sample
Issue -
State: open - Opened by Shettland 7 months ago
#253 - Enhance File Detection and Extend Compatibility for module read-bioinfo-metadata
Issue -
State: closed - Opened by Daniel-VM 7 months ago
Labels: enhancement
#252 - New process to upload the results from bioinformatics analysis back to sftp
Issue -
State: open - Opened by Shettland 7 months ago
Labels: enhancement
#251 - Update for laboratory addresses and minor changes in relecov_schema
Pull Request -
State: closed - Opened by Shettland 7 months ago
- 2 comments
#250 - Validation process does not distinguish "Not Provided" from empty values
Issue -
State: closed - Opened by Shettland 8 months ago
Labels: bug, enhancement
#249 - Validation process for single-end/paired-end reads
Issue -
State: closed - Opened by Shettland 8 months ago
Labels: bug, enhancement
#248 - Better documentation on how to use the tools
Issue -
State: closed - Opened by Shettland 8 months ago
Labels: documentation
#247 - Big changes in sftp_handle.py and minor in utils.py and configuration.json
Pull Request -
State: closed - Opened by Shettland 8 months ago
- 3 comments
#246 - Possible implementations in download module (sftp_handle.py)
Issue -
State: closed - Opened by Shettland 8 months ago
Labels: enhancement
#245 - New module required to process logs and send email
Issue -
State: closed - Opened by Shettland 8 months ago
Labels: enhancement
#244 - Future implementation to automate viralrecon execution
Issue -
State: closed - Opened by Shettland 8 months ago
#243 - Big changes in upload_ena_protocol, medium in read_bioinfo_metadata and map_schema and small changes in read_lab and configs
Pull Request -
State: closed - Opened by Shettland 9 months ago
#242 - Include handling of different md5 files
Issue -
State: closed - Opened by Shettland 9 months ago
Labels: enhancement
#241 - Handle ENA API timeouts in upload-to-ena module
Issue -
State: open - Opened by Shettland 10 months ago
- 1 comment
Labels: bug
#240 - Managing viralrecon execution
Issue -
State: closed - Opened by Shettland 10 months ago
- 7 comments
Labels: enhancement
#239 - Include automatic validation process after each step
Issue -
State: open - Opened by Shettland 10 months ago
Labels: enhancement
#238 - New ena-upload protocol and changes to map-schema, and read-metadata processes
Pull Request -
State: closed - Opened by Shettland about 1 year ago
- 1 comment
#237 - Changed local path for sftp_handle.py and introduced additional debug info
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#236 - Included new functionalities in download process to clean sftp server
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#235 - Included new fields into laboratory_address.json and geo_loc.json
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#234 - Fixed missing fields due to error in feed_database.py
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#233 - Changed sftp_handle to download everything in the output location.
Pull Request -
State: closed - Opened by Shettland over 1 year ago
- 1 comment
#232 - Included a new option in download process to select output location + minor comment changes
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#231 - Changes in schemas to simplify map_schema.py and to fix missing ontologies
Pull Request -
State: closed - Opened by Shettland over 1 year ago
- 1 comment
#230 - Group fields from configuration.json into different categories
Issue -
State: open - Opened by Shettland over 1 year ago
#229 - Changes in the json files related with read-lab-metadata.py along with adaptations of the code to the new structure
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#228 - Possible changes in the structure of the json files used in read_lab_metadata.py
Issue -
State: closed - Opened by Shettland over 1 year ago
#227 - Fixed read_lab_metadata.py to handle errors like missing data
Pull Request -
State: closed - Opened by Shettland over 1 year ago
#226 - Introduced new options to download function
Pull Request -
State: closed - Opened by Shettland over 1 year ago
- 5 comments
#225 - fixed error when sending several parameters via API
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#224 - Minor fixes feed database
Pull Request -
State: closed - Opened by saramonzon almost 2 years ago
#223 - fix label for variant designation in schema
Pull Request -
State: closed - Opened by saramonzon almost 2 years ago
#222 - Reviewing and fixing Bioinfo metadata module
Pull Request -
State: closed - Opened by saramonzon almost 2 years ago
#221 - Included collecting_institution, secuencing_data, GISAID and ENA fiel…
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#220 - Fixed bug in schema name and remove option to get other schema for feed database
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#219 - Fixes and changes in validate module
Pull Request -
State: closed - Opened by saramonzon almost 2 years ago
#218 - remove the self.headers in the PUT request
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#217 - Comments and some fixes
Pull Request -
State: closed - Opened by saramonzon almost 2 years ago
- 1 comment
#216 - fixed issue 215
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#215 - Invalid " table" field for "host subject id" and "study_type"
Issue -
State: closed - Opened by luissian almost 2 years ago
Labels: bug
#214 - fixed bug in long parse because changes in configuration json
Pull Request -
State: closed - Opened by luissian almost 2 years ago
#213 - Changes in gisaid metadata (gisaid_upload.py, relecov and gisaid schemas)
Pull Request -
State: closed - Opened by mlarjim almost 2 years ago
#212 - changes in gisaid_upload, __main__ and config json
Pull Request -
State: closed - Opened by mlarjim about 2 years ago
#211 - Actualizado el read bioinfo metadata y mas
Pull Request -
State: closed - Opened by luissian about 2 years ago
#210 - ena_schema.json vs relecov_schema.json y ena-upload-cli
Pull Request -
State: closed - Opened by ErikaKvalem about 2 years ago