Code

Release to 1.4.0#378

Code

Merged

OPSergio merged 72 commits intomainBU-ISCIII/relecov-tools:mainfrom developBU-ISCIII/relecov-tools:developCopy head branch name to clipboardJan 28, 2025

+726-134

Commits

Commits on Dec 30, 2024

• Added Ion 540 Chip Kit

  svarona

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  7f68e3b

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• Updated chengelog

  svarona

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• Added dev to version to keep in logfiles0

  svarona

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Commits on Jan 10, 2025

• Removed (*) in laboratory_address.json

  OPSergio

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• Removed (*) in the enum

  OPSergio

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• Merge pull request #365 from OPSergio/develop

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  OPSergio

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Commits on Jan 13, 2025

• Removed setup.py for pyproject.toml

  Shettland

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• Added dynamic-dependencies

  Shettland

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Commits on Jan 14, 2025

• Solved timeout upload_to_ena

  Aberdur

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  0d3cba7

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• Corrected blanks error

  Aberdur

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  2675202

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• Corrected blanks error

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  1303981

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• Corrected format error

  Aberdur

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  c8e15b1

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• Corrected format error

  Aberdur

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  cb71b5d

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• Merge branch 'develop' into develop

  Aberdur

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  aec7b8a

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• Merge pull request #369 from Aberdur/develop

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Commits on Jan 15, 2025

• Fixed path to files not containing sample name in basename

  svarona

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• Added batchID/date to filenames instead of date

  svarona

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• add current date to splitted files

  svarona

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• add year to outdir path

  svarona

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• test whether samples correspond to same batch date or not

  svarona

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  7526057

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• Added function to save splitted files to outdir

  svarona

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• test if bioinfo_lab_metadata exist, if exists merge

  svarona

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• Created code to merge metadata if already exist

  svarona

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  4fe8328

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• created function to search files containing muiltiple samples

  svarona

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  aa75429

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• test whether file exist and try to merge

  svarona

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  a8a5095

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• fixed black

  svarona

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  d7c7b61

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• Fixed flake8

  svarona

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  e9af243

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• fixed black

  svarona

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  13cf3e8

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• added creation of log in batch folder

  svarona

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  6c6a729

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• fixed regex to find long table in analysis_results

  svarona

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  8f07097

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• removed log that was not working

  svarona

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  04becc0

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• split files by batch first

  svarona

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  e86120c

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• created unique sufix for all files in batch

  svarona

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  a4ca40e

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• renamed save_splitted_files to save_merged_files

  svarona

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  1d4f777

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• added code to save splitted long table to batch dir

  svarona

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  436cb40

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• fixed black

  svarona

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  7785a11

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• added log errors

  svarona

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• replaced batch_id with batch_date

  svarona

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• replaced batch_id with batch_date

  svarona

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  4ff54fb

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• Updated changelog

  svarona

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  8570d3e

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• Added creation of analysis_results earlier for module to work

  svarona

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  9a94222

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• ignored flake error

  svarona

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  ec97363

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• flixed black and flake

  svarona

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  4417ce2

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• fixed black and flake

  svarona

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  2c61265

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• finally fixed flake8

  svarona

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  687b6a2

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• removed print

  svarona

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Commits on Jan 21, 2025

• Added log functionality in module build-schema

  Aberdur

  committed
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• Update CHANGELOG.md

  Aberdur

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  03683ba

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• black_lint corrected errors

  Aberdur

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• black_lint corrected errors

  Aberdur

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  54e759c

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• Merge pull request #371 from Aberdur/develop

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Commits on Jan 24, 2025

• Updated the metadata_processing field in configuration.json

  victor5lm

  committed
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• Added an "errors" field in the json schema

  victor5lm

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  de33f3f

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• Fixed bug

  victor5lm

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  ded81c5

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• Updated CHANGELOG.md

  victor5lm

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  6b276c5

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• Added other_preparation_kit, quality_control_metrics and consensus_criteria fields in the json schema

  victor5lm

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• Updated CHANGELOG.md

  victor5lm

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Commits on Jan 27, 2025

• Add QC to bioinfo_config.json

  Aberdur

  committed
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• Add QC functionality to read_bioinfo_metatada

  Aberdur

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• Add quality_control_evaluation to viralrecon.py

  Aberdur

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• Add QC fields to relecov_schema

  Aberdur

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  005b1d7

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• Update CHANGELOG.md

  Aberdur

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  f12162d

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• Update read_bioinfo_metadata black_lint

  Aberdur

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• Merge branch 'develop' into develop

  Aberdur

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• Merge pull request #373 from Aberdur/develop

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  27597b0

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• Added dropdown functionality to build-schema

  Aberdur

  committed
  287fd34

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• Update CHANGELOG.md

  Aberdur

  committed
  21b1d3c

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• Solve flake8

  Aberdur

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Commits on Jan 28, 2025

• Updated version to 1.4.0

  OPSergio

  committed
  aa6d234

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• Updated version in CHANGELOG.md

  OPSergio

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  0b86cf1

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• Updated link version

  OPSergio

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• Updated version in .toml

  OPSergio

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