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

#332 - Add library kit

Pull Request - State: closed - Opened by OPSergio 19 days ago - 1 comment

#329 - Logs-to-excel accepts multiple keys and includes folder logs

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

#328 - Mail sender

Pull Request - State: open - Opened by OPSergio about 1 month ago - 1 comment

#327 - Release 1.2.0

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

#326 - Request for access to the REGCESS database.

Issue - State: open - Opened by OPSergio about 2 months ago

#325 - Pipeline-manager should take into consideration different primer versions

Issue - State: closed - Opened by Shettland about 2 months ago - 1 comment
Labels: bug, enhancement

#324 - Pre-release 1.2.0

Pull Request - State: closed - Opened by Shettland about 2 months ago

#323 - Improvement: add date to launch-pipeline

Issue - State: closed - Opened by svarona about 2 months ago - 1 comment

#322 - New wrapper module & changes in logs reporting

Pull Request - State: closed - Opened by Shettland about 2 months ago

#321 - Hotfix for download_manager & enhancements for pipeline-manager

Pull Request - State: closed - Opened by Shettland about 2 months ago

#320 - Actions workflows and datasets minor changes

Pull Request - State: closed - Opened by Shettland about 2 months ago

#319 - tmp_processing folder not being renamed to invalid_samples

Issue - State: closed - Opened by svarona about 2 months ago - 1 comment

#318 - Read-lab-metadata search for files recursively when no samples_data is given

Issue - State: open - Opened by Shettland about 2 months ago - 1 comment
Labels: enhancement

#317 - Mail module

Issue - State: open - Opened by OPSergio about 2 months ago - 1 comment

#316 - Añadido Hospital Universitari Doctor Josep Trueta

Pull Request - State: closed - Opened by OPSergio 2 months ago

#315 - Included Hospital Universitario Araba in laboratory_address.json

Pull Request - State: closed - Opened by juanledesma78 2 months ago - 2 comments

#312 - Github actions fixes, test-sftp-handle and pypi_publish

Pull Request - State: closed - Opened by Shettland 2 months ago

#311 - Merge changes from main into develop

Pull Request - State: closed - Opened by Shettland 2 months ago

#310 - upload to GitHub Release is no longer needed in pypi_publish

Issue - State: closed - Opened by Shettland 2 months ago
Labels: bug

#309 - Release v1.1.0

Pull Request - State: closed - Opened by Shettland 2 months ago

#308 - Pre-release 1.1.0. Includes fixing github actions

Pull Request - State: closed - Opened by Shettland 2 months ago

#307 - bioinfo_config.json documentation

Issue - State: open - Opened by Shettland 2 months ago
Labels: documentation

#306 - Now read-bioinfo-metadata splits data and extract files for each batch

Pull Request - State: closed - Opened by Shettland 2 months ago - 1 comment

#305 - Merge pull request #298 from BU-ISCIII/develop

Pull Request - State: closed - Opened by Shettland 2 months ago

#304 - fix minor bug launch pipeline for copying r2

Pull Request - State: closed - Opened by saramonzon 3 months ago

#303 - Fixes and improvements in launch_pipeline

Pull Request - State: closed - Opened by saramonzon 3 months ago

#302 - Create a wrapper that launches download, read-lab-metadata and validate

Issue - State: closed - Opened by Shettland 3 months ago - 1 comment
Labels: enhancement

#301 - Fix test_sftp_handle workflow concurrency issues

Issue - State: closed - Opened by Shettland 3 months ago - 1 comment
Labels: bug

#300 - log_summary creates an excel file from logs

Pull Request - State: closed - Opened by Shettland 3 months ago - 2 comments

#299 - Included pango-data version extraction in read-bioinfo-metadata

Pull Request - State: closed - Opened by Shettland 3 months ago - 2 comments

#298 - Release 1.0.0

Pull Request - State: closed - Opened by Shettland 3 months ago

#297 - Add upload_database tests to github actions

Issue - State: open - Opened by Shettland 3 months ago
Labels: enhancement

#296 - Pre-release changes for version 1.0.0

Pull Request - State: closed - Opened by Shettland 3 months ago

#295 - upload database module updated

Pull Request - State: closed - Opened by luissian 3 months ago - 2 comments

#294 - Add Build Schema Test to GitHub Actions

Issue - State: open - Opened by Daniel-VM 3 months ago

#292 - fixing bugs on pipeline manager

Pull Request - State: closed - Opened by luissian 3 months ago

#291 - Include data_validation in template

Issue - State: open - Opened by Shettland 3 months ago
Labels: enhancement

#290 - read-lab date parse hotfix

Pull Request - State: closed - Opened by Shettland 3 months ago

#289 - Hotfix for invalid date check in read-lab-metadata

Pull Request - State: closed - Opened by Shettland 3 months ago

#288 - Standardize output filenames

Pull Request - State: closed - Opened by Shettland 3 months ago

#287 - Created new class SFTPRelecov for sftp functions

Pull Request - State: closed - Opened by luissian 3 months ago

#286 - issue 284. created new module for pipeline launch

Pull Request - State: closed - Opened by luissian 4 months ago - 1 comment

#284 - Create an option to create simbolic links to Analisys folder

Issue - State: closed - Opened by luissian 4 months ago
Labels: enhancement

#283 - Convert custom logs to xlsx format

Issue - State: closed - Opened by Shettland 4 months ago
Labels: enhancement

#282 - Log_summary could output the generated custom log in a folder named "logs"

Issue - State: open - Opened by Shettland 4 months ago
Labels: enhancement

#281 - Updated log_summary.py with new path field and renamed keys

Pull Request - State: closed - Opened by Shettland 4 months ago

#280 - Better sftp cleaning and download logging

Pull Request - State: closed - Opened by Shettland 4 months ago

#279 - Validate module now creates a validated metadata json file

Pull Request - State: closed - Opened by Shettland 4 months ago

#278 - Now json_summary custom log filename includes module called

Pull Request - State: closed - Opened by Shettland 4 months ago

#276 - Include a test for file integrity somewhere in the workflow

Issue - State: closed - Opened by Shettland 5 months ago - 1 comment
Labels: enhancement

#275 - Missing fields when read-bioinfo-metadata is executed

Issue - State: closed - Opened by Shettland 5 months ago
Labels: bug

#274 - Create validated.json keeping only samples that passed validation process

Issue - State: closed - Opened by Shettland 5 months ago
Labels: enhancement

#273 - New module `build_schema`

Pull Request - State: closed - Opened by Daniel-VM 5 months ago - 3 comments

#272 - Enhance json schema validation with custom validators

Pull Request - State: open - Opened by Daniel-VM 5 months ago - 1 comment

#271 - Enhance JSON Schema validation with custom validators for complex propertyIDs

Issue - State: open - Opened by Daniel-VM 5 months ago
Labels: enhancement

#270 - test

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

#269 - Hotfix for tmp folder creation in remote home

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

#268 - Automatically send email of process log summary to the lab

Issue - State: open - Opened by Shettland 6 months ago
Labels: enhancement

#267 - Read-bioinfo-metadata creates output even with no matching samples

Issue - State: open - Opened by Shettland 6 months ago
Labels: bug

#266 - Changing how analysis_date is collected from variants_long_table

Issue - State: closed - Opened by Shettland 6 months ago - 1 comment
Labels: enhancement

#265 - Fixed actions pull-requests error again

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

#264 - Splitted tests in two files, fixed pull-request checkout error

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

#263 - Changing all the enums in each schema to lowercase

Issue - State: open - Opened by Shettland 6 months ago

#260 - update read-bioinfo-metadata readme

Pull Request - State: closed - Opened by Daniel-VM 7 months ago

#258 - Refactor of read-bioinfo-metadata module for tool compatibility expansion

Pull Request - State: closed - Opened by Daniel-VM 8 months ago - 3 comments

#257 - Small fix of tests and blood included in anatomical material

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

#256 - New workflow to test modules and new testing dataset

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

#254 - Unique identifier for each sample

Issue - State: open - Opened by Shettland 9 months ago - 1 comment
Labels: bug

#253 - Enhance File Detection and Extend Compatibility for module read-bioinfo-metadata

Issue - State: closed - Opened by Daniel-VM 9 months ago
Labels: enhancement

#252 - New process to upload the results from bioinformatics analysis back to sftp

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

#251 - Update for laboratory addresses and minor changes in relecov_schema

Pull Request - State: closed - Opened by Shettland 9 months ago - 2 comments

#250 - Validation process does not distinguish "Not Provided" from empty values

Issue - State: closed - Opened by Shettland 10 months ago
Labels: bug, enhancement

#249 - Validation process for single-end/paired-end reads

Issue - State: closed - Opened by Shettland 10 months ago
Labels: bug, enhancement

#248 - Better documentation on how to use the tools

Issue - State: closed - Opened by Shettland 10 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 10 months ago - 3 comments

#246 - Possible implementations in download module (sftp_handle.py)

Issue - State: closed - Opened by Shettland 11 months ago
Labels: enhancement

#245 - New module required to process logs and send email

Issue - State: closed - Opened by Shettland 11 months ago
Labels: enhancement

#244 - Future implementation to automate viralrecon execution

Issue - State: closed - Opened by Shettland 11 months ago

#242 - Include handling of different md5 files

Issue - State: closed - Opened by Shettland 11 months ago
Labels: enhancement

#241 - Handle ENA API timeouts in upload-to-ena module

Issue - State: open - Opened by Shettland about 1 year ago - 1 comment
Labels: bug

#240 - Managing viralrecon execution

Issue - State: closed - Opened by Shettland about 1 year ago - 7 comments
Labels: enhancement

#239 - Include automatic validation process after each step

Issue - State: closed - Opened by Shettland about 1 year ago
Labels: enhancement

#238 - New ena-upload protocol and changes to map-schema, and read-metadata processes

Pull Request - State: closed - Opened by Shettland over 1 year ago - 1 comment

#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