BU-ISCIII/relecov-tools issues and pull requests

#309 - Release v1.1.0

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

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

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

#307 - bioinfo_config.json documentation

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

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

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

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

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

#304 - fix minor bug launch pipeline for copying r2

Pull Request - State: closed - Opened by saramonzon 8 days ago

#303 - Fixes and improvements in launch_pipeline

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

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

Issue - State: open - Opened by Shettland 13 days ago
Labels: enhancement

#301 - Fix test_sftp_handle workflow concurrency issues

Issue - State: open - Opened by Shettland 14 days ago
Labels: bug

#300 - log_summary creates an excel file from logs

Pull Request - State: closed - Opened by Shettland 14 days ago - 2 comments

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

Pull Request - State: closed - Opened by Shettland 14 days ago - 2 comments

#298 - Release 1.0.0

Pull Request - State: closed - Opened by Shettland 16 days ago

#297 - Add upload_database tests to github actions

Issue - State: open - Opened by Shettland 16 days ago
Labels: enhancement

#296 - Pre-release changes for version 1.0.0

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

#295 - upload database module updated

Pull Request - State: closed - Opened by luissian 20 days ago - 2 comments

#294 - Add Build Schema Test to GitHub Actions

Issue - State: open - Opened by Daniel-VM 21 days ago

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

Issue - State: open - Opened by Daniel-VM 21 days ago

#292 - fixing bugs on pipeline manager

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

#291 - Include data_validation in template

Issue - State: open - Opened by Shettland 25 days ago
Labels: enhancement

#290 - read-lab date parse hotfix

Pull Request - State: closed - Opened by Shettland 27 days ago

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

Pull Request - State: closed - Opened by Shettland 27 days ago

#288 - Standardize output filenames

Pull Request - State: closed - Opened by Shettland 27 days ago

#287 - Created new class SFTPRelecov for sftp functions

Pull Request - State: closed - Opened by luissian 28 days 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 5 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 7 months ago
Labels: bug, enhancement

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

Issue - State: closed - Opened by Shettland 7 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