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Release to 1.4.0 #378

Merged
merged 72 commits into from
Jan 28, 2025
Merged

Release to 1.4.0 #378

merged 72 commits into from
Jan 28, 2025

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OPSergio
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Added enhancements

  • Added a IonTorrent flow cell for validation #363
  • Added solution to timeout in upload-to-ena module #368
  • Added log functionality to build-schema module #340
  • Updated the metadata_processing field in configuration.json and added the other_preparation_kit, quality_control_metrics and consensus_criteria fields in the json schema #372
  • Added quality control functionality to read-bioinfo-metadata #373
  • Added dropdown functionality to build-schema enums #374

Fixes

  • Fixed read-bioinfo-metadata module #367

svarona and others added 30 commits December 30, 2024 18:09
@svarona
Added Ion 540 Chip Kit
7f68e3b
@svarona
Updated chengelog
3c349a1
@svarona
Added dev to version to keep in logfiles0
4936b7c
@OPSergio
Removed (*) in laboratory_address.json
58bdfe0
@OPSergio
Removed (*) in the enum
6d80436
@OPSergio
Merge pull request #365 from OPSergio/develop
dd5c287 
Removed (*) in laboratory_address.json
@Shettland
Removed setup.py for pyproject.toml
304ff6e
@Shettland
Added dynamic-dependencies
7953cf4
@Aberdur
Solved timeout upload_to_ena
0d3cba7
@Aberdur
Corrected blanks error
2675202
@Aberdur
Corrected blanks error
1303981
@Aberdur
Corrected format error
c8e15b1
@Aberdur
Corrected format error
cb71b5d
@Aberdur
Merge branch 'develop' into develop
aec7b8a
@Aberdur
Merge pull request #369 from Aberdur/develop
64a54cf 
Solved timeout upload_to_ena
@svarona
Fixed path to files not containing sample name in basename
513789e
@svarona
Added batchID/date to filenames instead of date
a5a164f
@svarona
add current date to splitted files
3d9e962
@svarona
add year to outdir path
1b316d4
@svarona
test whether samples correspond to same batch date or not
7526057
@svarona
Added function to save splitted files to outdir
103248e
@svarona
test if bioinfo_lab_metadata exist, if exists merge
aac4937
@svarona
Created code to merge metadata if already exist
4fe8328
@svarona
created function to search files containing muiltiple samples
aa75429
@svarona
test whether file exist and try to merge
a8a5095
@svarona
fixed black
d7c7b61
@svarona
Fixed flake8
e9af243
@svarona
fixed black
13cf3e8
@svarona
added creation of log in batch folder
6c6a729
@svarona
fixed regex to find long table in analysis_results
8f07097
svarona and others added 27 commits January 15, 2025 17:08
@svarona
removed print
030fd3a
@Aberdur
Added log functionality in module build-schema
d444f4f
@Aberdur
Update CHANGELOG.md
03683ba
@Aberdur
black_lint corrected errors
3fd902e
@Aberdur
black_lint corrected errors
54e759c
@Aberdur
Merge pull request #371 from Aberdur/develop
85afe5b 
Added log functionality in build-schema module
@victor5lm
Updated the metadata_processing field in configuration.json
42fd6d8
@victor5lm
Added an "errors" field in the json schema
de33f3f
@victor5lm
Fixed bug
ded81c5
@victor5lm
Updated CHANGELOG.md
6b276c5
@victor5lm
Added other_preparation_kit, quality_control_metrics and consensus_cr…
03f534a 
…iteria fields in the json schema
@victor5lm
Updated CHANGELOG.md
c2eb5d4
@Aberdur
Add QC to bioinfo_config.json
df5c673
@Aberdur
Add QC functionality to read_bioinfo_metatada
bb40eb3
@Aberdur
Add quality_control_evaluation to viralrecon.py
66f936c
@Aberdur
Add QC fields to relecov_schema
005b1d7
@Aberdur
Update CHANGELOG.md
f12162d
@Aberdur
Update read_bioinfo_metadata black_lint
bd69996
@Aberdur
Merge branch 'develop' into develop
8291c79
@Aberdur
Merge pull request #373 from Aberdur/develop
27597b0 
Added Quality Control functionality to read-bioinfo-metadata module
@Aberdur
Added dropdown functionality to build-schema
287fd34
@Aberdur
Update CHANGELOG.md
21b1d3c
@Aberdur
Solve flake8
fe51b1d
@OPSergio
Updated version to 1.4.0
aa6d234
@OPSergio
Updated version in CHANGELOG.md
0b86cf1
@OPSergio
Updated link version
94919ff
@OPSergio
Updated version in .toml
367873e
@OPSergio OPSergio merged commit 607e792 into main Jan 28, 2025
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@Aberdur Aberdur Aberdur approved these changes

@saramonzon saramonzon saramonzon approved these changes

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6 participants
@OPSergio @saramonzon @Aberdur @svarona @Shettland @victor5lm