Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release/v2.2.0 #36

Merged
merged 83 commits into from
Jun 18, 2024
Merged

Release/v2.2.0 #36

merged 83 commits into from
Jun 18, 2024

Conversation

ALuesink
Copy link
Contributor

Release v2.2.0 (DIMS) to main

mraves2 and others added 30 commits June 30, 2023 10:47
@mraves2
added functionality for AssignToBins
b28bfd3
@mraves2
added functionality for GenerateBreaks
dcbfbcf
@mraves2
reference to old file added
ca3ae44
@mraves2
added functionality for MakeInit file
0e66635
@mraves2
added new files
e5a0154
@mraves2
added ThermoRawFileParser.nf to CustomModules
5461f86
@mraves2
added file for listing of raw files
0d8f0f0
@mraves2
new files added, existing files modified
4c29eb8
@mraves2
code cleaned up
6b6c531
@mraves2
added functionality
39e2cb7
@mraves2
modified files for Nextflow
ab5c457
@mraves2
extra files for Nextflow pipeline
6d54b14
@mraves2
modified files and added new files
03edd32
@mraves2
first working version of full NF pipeline
657a7cd
@mraves2
added parameter for measurements with high m/z
1aa51e0
@mraves2
added modification of threshold in case of high m/z
f973a23
@ellendejong
Add EditSummaryFileHappy
e41ea88
@ellendejong
refactor script in EditSummaryFileHappy
a70501c
@ellendejong
add joined column of truth and query samples
c20d8f8
@ellendejong
add delim
d8c0bc0
@ellendejong
change column to Type and Filter
78c04e7
@ellendejong
use meta.id as tag
eb55d6b
@ellendejong
add stageAs to CheckQC
240008c
@ellendejong
typo
56093d4
@mraves2
used lintr and styler to clean up code
1036d57
@ellendejong
convert qc_value to float
2996892
@ellendejong
change input to qc settings metrics
6177ce9
@ellendejong
Add docstrings checkqc
e162db0
@ellendejong
Split awk and rename output
e5e3acb
@ellendejong
Only add .* if string is provided
7d03db3
ALuesink and others added 24 commits April 16, 2024 09:40
@ALuesink
Cleaned up GenerateViolinPlots AddOnFunctions
038521d
@ALuesink
Output paths added
b75faba
@ALuesink
Changed to Unidentified steps to parallel
3687f14
@ALuesink
Added changes HPC and parallelisation Unidentified
7187c2f
@ALuesink
Added loading package
f933561
@ALuesink
Changed output
8397c12
@mraves2
cleaned up peak finding, fill missing functions
507c88d
@ALuesink
TIC plots and TRFP flag
0a81719
@ALuesink
Fix TIC plot pdf
4041d97
@mraves2
corrected error in aggregate lines
2089bab
@mraves2
code review changes applied
a9c267c
@mraves2
code review changes applied
79bc26a
@mraves2
fixed names of Utils function calls
40da954
@ALuesink
Added Zscore if statement
c37ddb8
@ALuesink
Fixed missing negative HMDB part
3f7b690
@mraves2
code review changes applied
b7b56d8
@mraves2
code review changes applied
72e53d5
@ALuesink
Changes for using Utils
c7b44f6
@rernst
Merge pull request #32 from UMCUGenetics/feature/update_flask_tools
af7164b 
Feature/update flask tools to dev
@rernst
Merge pull request #34 from UMCUGenetics/hotfix/v2.1.2
ca633e4 
Hotfix/v2.1.2 to dev
@rernst
Revert "Feature/giabeval"
3a0fcbb
@rernst
Merge pull request #35 from UMCUGenetics/revert-21-feature/giabeval
4c0c967 
Revert "Feature/giabeval"
@ALuesink
Merge pull request #22 from UMCUGenetics/feature/DIMS
7c29531 
Feature/dims
@ALuesink
Merge branch 'develop' into release/v2.2.0
9e114c4
@rernst rernst self-requested a review June 18, 2024 08:32
rernst
rernst approved these changes Jun 18, 2024
View reviewed changes
Copy link
Member

@rernst rernst left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Reviewed in #22 and revert giab eval changes in #35.

@ALuesink ALuesink merged commit 972a97e into main Jun 18, 2024
@rernst rernst deleted the release/v2.2.0 branch June 18, 2024 08:33
@ALuesink ALuesink restored the release/v2.2.0 branch July 8, 2024 12:02
@ALuesink ALuesink deleted the release/v2.2.0 branch July 8, 2024 14:09
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@rernst rernst rernst approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@ALuesink @rernst @mraves2 @ellendejong @BasMonkey