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New release #198

Merged
merged 230 commits into from
Nov 8, 2024
Merged

New release #198

merged 230 commits into from
Nov 8, 2024

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LaurenceKuhl
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v2.3.0 - Lime Nightingale - [17.09.2024]

Added

  • Add module to classify samples by clonality (#178)
  • Add DrugZ, a module for chemogenetic interaction (#168)
  • Add Hitselection, a module for subsetting more likely true positives for KO screen based on the protein protein interaction (#191)
  • Make the use of gene essentiality module more user friendly and readable in the code (#194)

Fixed

  • Fix cutadapt 3' and 5' no such variable found bug (#187)
  • Fix design matrix bug that introduced dots instead of a hyphen (#190)
  • Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty (#190)
  • Fix a typo in crisprcleanr/normalize, when a user inputs a file (#192)

Metin Yazar and others added 30 commits February 28, 2024 12:28
drugz first commit
458d1d8
drugz second commit
8a21317
DrugZ_template_lint
4a14dee
foldchange_added
d2eb3b1
drugz removed
f9fd4fd
Merge remote-tracking branch 'upstream/master'
4f3b6ac
@LaurenceKuhl
Merge branch 'dev' into master
e95e0bc
@LaurenceKuhl
Add removal of genes in drugZ with an extra parameter
cd42df3
@LaurenceKuhl
Add option of removal of genes
15f4a6d
@alan-tracey
Create clonality_classifier.nf
979638b
@alan-tracey
Update clonality_classifier.nf
d11ef15
@alan-tracey
Create indel_classifier.py
f0d94c1
@alan-tracey
Update indel_classifier.py
1d0e5c3
@alan-tracey
Update clonality_classifier.nf
e30b89b
@alan-tracey
Update clonality_classifier.nf
63bc7d4
@alan-tracey
Update clonality_classifier.nf
b53f628
@alan-tracey
Update clonality_classifier.nf
fb37547
@mirpedrol
Merge branch 'dev' into master
b66ea4b
@alan-tracey @mirpedrol
Update modules/local/clonality_classifier.nf
e6d1f87 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@alan-tracey @mirpedrol
Update templates/indel_classifier.py
d9decb8 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@alan-tracey @mirpedrol
Update templates/indel_classifier.py
9e5c469 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@alan-tracey @mirpedrol
Update templates/indel_classifier.py
baa901a 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@alan-tracey
Update crisprseq_targeted.nf
03a6cf9
@mirpedrol
add @alan-tracey to contributors list
4d43db7
@mirpedrol
publish classify_clonality versions and output file to publish dir
40063e0
@mirpedrol
add parameter skip_clonality
37c75c1
@mirpedrol
Apply suggestions from code review
f779bf6
@nf-core-bot
[automated] Fix code linting
e70b118
@mirpedrol
fix module name and container
adab60a
@mirpedrol
more fixes
8f9312f
mashehu and others added 29 commits October 17, 2024 12:40
@mashehu
fix resourceLimits
9fb3903
@LaurenceKuhl
Merge pull request #210 from nf-core/manual-template-update-3_0_2
1966d85 
Manual-template-update-3_0_2
@mirpedrol
Merge branch 'dev' into add-more-tests
be3bdc4
@mirpedrol
fix bug in ci.yml
51b28fb
@mirpedrol
fix default medaka_model in json schema
8e8653e
@LaurenceKuhl
Update templates/template_fluteMLE.R
36ba081
@LaurenceKuhl
Merge pull request #185 from mirpedrol/add-more-tests
c3f7184 
run pipeline tests with singularity and conda too
@LaurenceKuhl
Fix conda issues
9157248
@LaurenceKuhl
Merge branch 'dev' into dev
a9774f1
@mirpedrol
uncomment including pipeline config
cfb11a7
@LaurenceKuhl
Merge pull request #212 from LaurenceKuhl/dev
28d66c8 
Fix conda issues
@LaurenceKuhl
Merge branch 'dev' into fix-linting
d95cefc
@mirpedrol
Merge pull request #213 from mirpedrol/fix-linting
eacc5e7 
uncomment including pipeline config
@LaurenceKuhl
Try to fix RRA
886228c
@LaurenceKuhl
Merge branch 'dev' into dev
b345455
@LaurenceKuhl
Add singularity to the CI
45eb416
@LaurenceKuhl
Merge branch 'dev' of github.com:laurencekuhl/crisprseq into dev
a0b30ee
@LaurenceKuhl
Add temp location
1ea9a93
@mirpedrol
try defining BIOMART_CACHE for mageck flute
c6f5c19
@medmaca
Modified to fix template_fluteMLE.R for Apptainer/Singularity
9f0de4f
@medmaca
Modified graphrra.nf for Apptainer/Singularity.
84a919a
@LaurenceKuhl
pre commit
39f5f54
@LaurenceKuhl
Update changelog
a7bc829
@LaurenceKuhl
Add Matthew as a conntributer
5316dc9
@LaurenceKuhl
Update .github/workflows/ci.yml
957b5f2
@LaurenceKuhl
Merge pull request #214 from LaurenceKuhl/dev
be6922e 
Fix MAGeCKFlute issues
@LaurenceKuhl
put in the right date for the the release (finally) (template update …
f91f470 
…omg)
@LaurenceKuhl
Merge branch 'nf-core:dev' into dev
9ea138e
@LaurenceKuhl
Merge pull request #215 from LaurenceKuhl/dev
72afaab 
put the right date for the release yayyyy
@LaurenceKuhl LaurenceKuhl merged commit 0e9f915 into master Nov 8, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@LaurenceKuhl @JoseEspinosa @mirpedrol @alan-tracey @nf-core-bot @joannakraw @mashehu @medmaca