Ecosyste.ms: Issues

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GitHub / BU-ISCIII/relecov-tools issues and pull requests

#376 - Release 1.4.0

Pull Request - State: open - Opened by OPSergio 11 days ago

#375 - Added drop-down functionality to build-schema

Pull Request - State: closed - Opened by Aberdur 12 days ago

#372 - Updated configuration.json and the json schema

Pull Request - State: closed - Opened by victor5lm 15 days ago

#371 - Added log functionality in build-schema module

Pull Request - State: closed - Opened by Aberdur 18 days ago

#370 - Rewrite read-bioinfo metadata module

Issue - State: open - Opened by svarona 23 days ago

#369 - Solved timeout upload_to_ena

Pull Request - State: closed - Opened by Aberdur 25 days ago

#368 - Make metadata homogeneizer work properly

Pull Request - State: open - Opened by Shettland 25 days ago

#367 - Fixed read-bioinfo-metadata module

Pull Request - State: closed - Opened by svarona 26 days ago

#366 - Removed setup.py for pyproject.toml

Pull Request - State: closed - Opened by Shettland 28 days ago

#365 - Removed (*) in laboratory_address.json

Pull Request - State: closed - Opened by OPSergio 29 days ago

#364 - Create toml file

Issue - State: closed - Opened by saramonzon about 1 month ago

#363 - Added Ion 540 Chip Kit to schema

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

#362 - Updated release date

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

#361 - Fixed email module

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

#360 - Allow to use a .txt file for email

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

#359 - .fastq file repeated in metadata

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

#358 - Review IonTorrent and Nanopore ontologies

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

#357 - Fixing validate crashing with new sheet names

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

#356 - added a sample with corrupted gzip for testing

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

#354 - Fixed some issues in download module

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

#353 - Sometimes rx_md5 fields are filled with null

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

#352 - ESRI data base

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

#351 - Longtable.json should be created in output-directory

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

#350 - " Analysis date " duplicate label in the schema

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

#349 - Mail module enhanced

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

#348 - Removed duplicated sequence/fastq_md5

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

#347 - Update read-bioinfo-metadata to include quality control checks

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

#346 - Add a github actions test for the wrapper

Issue - State: open - Opened by svarona 2 months ago

#345 - Wrapper fails to create excel files

Issue - State: open - Opened by svarona 2 months ago

#344 - Corrupted samples aren't removed from samples_data_*.json

Issue - State: closed - Opened by svarona 2 months ago - 2 comments

#343 - Release v1.3.0

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

#342 - Hotfix for folder-names arg in pipeline-manager

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

#341 - pipeline-manager batch folder name is taking time

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

#340 - Hospital fixes

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

#339 - Pre-release 1,3,0

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

#338 - Linaje analysis date is not defined in the schema

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

#337 - duplicate md5 information in the schema

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

#336 - Add relecov-tools version to log-file

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

#335 - Fixed linting was still waiting for .py files

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

#333 - Add SQK-RBK114-96 to library_preparation_kit schema

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

#332 - Add library kit

Pull Request - State: closed - Opened by OPSergio 3 months ago - 1 comment

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

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

#328 - Mail sender

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

#327 - Release 1.2.0

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

#326 - Request for access to the REGCESS database.

Issue - State: open - Opened by OPSergio 4 months ago

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

Issue - State: closed - Opened by Shettland 4 months ago - 1 comment
Labels: bug, enhancement

#324 - Pre-release 1.2.0

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

#323 - Improvement: add date to launch-pipeline

Issue - State: closed - Opened by svarona 4 months ago - 1 comment

#322 - New wrapper module & changes in logs reporting

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

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

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

#320 - Actions workflows and datasets minor changes

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

#319 - tmp_processing folder not being renamed to invalid_samples

Issue - State: closed - Opened by svarona 4 months ago - 1 comment

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

Issue - State: closed - Opened by Shettland 4 months ago - 1 comment
Labels: enhancement

#317 - Mail module

Issue - State: closed - Opened by OPSergio 4 months ago - 1 comment

#316 - Añadido Hospital Universitari Doctor Josep Trueta

Pull Request - State: closed - Opened by OPSergio 5 months ago

#315 - Included Hospital Universitario Araba in laboratory_address.json

Pull Request - State: closed - Opened by juanledesma78 5 months ago - 2 comments

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

Pull Request - State: closed - Opened by Shettland 5 months ago

#311 - Merge changes from main into develop

Pull Request - State: closed - Opened by Shettland 5 months ago

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

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

#309 - Release v1.1.0

Pull Request - State: closed - Opened by Shettland 5 months ago

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

Pull Request - State: closed - Opened by Shettland 5 months ago

#307 - bioinfo_config.json documentation

Issue - State: open - Opened by Shettland 5 months ago
Labels: documentation

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

Pull Request - State: closed - Opened by Shettland 5 months ago - 1 comment

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

Pull Request - State: closed - Opened by Shettland 5 months ago

#304 - fix minor bug launch pipeline for copying r2

Pull Request - State: closed - Opened by saramonzon 5 months ago

#303 - Fixes and improvements in launch_pipeline

Pull Request - State: closed - Opened by saramonzon 5 months ago

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

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

#301 - Fix test_sftp_handle workflow concurrency issues

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

#300 - log_summary creates an excel file from logs

Pull Request - State: closed - Opened by Shettland 5 months ago - 2 comments

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

Pull Request - State: closed - Opened by Shettland 5 months ago - 2 comments

#298 - Release 1.0.0

Pull Request - State: closed - Opened by Shettland 5 months ago

#297 - Add upload_database tests to github actions

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

#296 - Pre-release changes for version 1.0.0

Pull Request - State: closed - Opened by Shettland 5 months ago

#295 - upload database module updated

Pull Request - State: closed - Opened by luissian 5 months ago - 2 comments

#294 - Add Build Schema Test to GitHub Actions

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

#293 - Lack of `--log-file` core functionality in module `build-schema`

Issue - State: closed - Opened by Daniel-VM 5 months ago - 1 comment

#292 - fixing bugs on pipeline manager

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

#291 - Include data_validation in template

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

#290 - read-lab date parse hotfix

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

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

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

#288 - Standardize output filenames

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

#287 - Created new class SFTPRelecov for sftp functions

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

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

Pull Request - State: closed - Opened by luissian 6 months ago - 1 comment

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

Issue - State: closed - Opened by luissian 7 months ago
Labels: enhancement

#283 - Convert custom logs to xlsx format

Issue - State: closed - Opened by Shettland 7 months ago
Labels: enhancement

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

Issue - State: closed - Opened by Shettland 7 months ago
Labels: enhancement

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

Pull Request - State: closed - Opened by Shettland 7 months ago

#280 - Better sftp cleaning and download logging

Pull Request - State: closed - Opened by Shettland 7 months ago

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

Pull Request - State: closed - Opened by Shettland 7 months ago

#278 - Now json_summary custom log filename includes module called

Pull Request - State: closed - Opened by Shettland 7 months ago