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Add BAGEL2 functionality #60

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merged 46 commits into from
Nov 7, 2023
Merged

Add BAGEL2 functionality #60

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8f6af2d
Extra files from mageck count
LaurenceKuhl Jul 14, 2023
13181f0
fix bug in rra
LaurenceKuhl Jul 14, 2023
b66f7e5
Add bagel fold change
LaurenceKuhl Jul 21, 2023
4faa210
Merge remote-tracking branch 'source_repo/dev' into bump
LaurenceKuhl Jul 21, 2023
ac2ca2c
Trying to add BAGEL_BF
LaurenceKuhl Jul 27, 2023
8a88803
Adding bagel2_bf
LaurenceKuhl Jul 28, 2023
0bebd94
working modules of bagel
LaurenceKuhl Jul 31, 2023
a6d4090
All of the bagel modules and output graphs
LaurenceKuhl Aug 1, 2023
6ef05ac
Bagel2
LaurenceKuhl Aug 8, 2023
7030145
Add new features in changelog
LaurenceKuhl Aug 8, 2023
5be5815
Fixed paired-end
LaurenceKuhl Aug 8, 2023
1d2dff0
Merge branch 'dev' into bump
mirpedrol Aug 8, 2023
2519663
Update CHANGELOG.md
LaurenceKuhl Aug 9, 2023
65c0f6f
Update CHANGELOG.md
LaurenceKuhl Aug 9, 2023
2be7f3b
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 9, 2023
ea07b75
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 9, 2023
9278293
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 9, 2023
4cc4bba
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 9, 2023
d0b21d9
formatting
LaurenceKuhl Aug 9, 2023
ce6c7ee
Merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…
LaurenceKuhl Aug 9, 2023
6c8993b
test
LaurenceKuhl Aug 9, 2023
29dc2bd
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 9, 2023
f8210a4
Add doc
LaurenceKuhl Aug 16, 2023
e21fc25
fix meta id
LaurenceKuhl Aug 16, 2023
63f328a
Ran nf-core modules patch
LaurenceKuhl Aug 16, 2023
90eb287
Add license
LaurenceKuhl Aug 16, 2023
0d7aeb4
Update workflows/crisprseq_screening.nf
LaurenceKuhl Aug 23, 2023
6b75dd9
Add license
LaurenceKuhl Aug 24, 2023
1bf922d
Merge branch 'dev' into bump
LaurenceKuhl Aug 24, 2023
f2576c4
Remove symlink issue
LaurenceKuhl Oct 2, 2023
5d343af
Update module config
LaurenceKuhl Oct 2, 2023
31a1103
Add graphs for mageck rra
LaurenceKuhl Oct 24, 2023
fef0481
Update docs/usage/screening.md
LaurenceKuhl Oct 25, 2023
77f2509
Update workflows/crisprseq_screening.nf
LaurenceKuhl Oct 25, 2023
acd150d
Modifications suggested by Julia
LaurenceKuhl Oct 25, 2023
0fefa45
merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…
LaurenceKuhl Oct 25, 2023
718ceaa
Take comments into account add license
LaurenceKuhl Oct 25, 2023
2a756b8
Add contrast file in the test
LaurenceKuhl Nov 3, 2023
4a95736
remove condition
LaurenceKuhl Nov 3, 2023
9d67bd0
rollback on the condition in the samplesheet
LaurenceKuhl Nov 7, 2023
00d0d16
[automated] Fix linting with Prettier
nf-core-bot Nov 7, 2023
0049dde
ran prettier
LaurenceKuhl Nov 7, 2023
fdc1c2c
Merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…
LaurenceKuhl Nov 7, 2023
e073518
nf-core modules patch on mageck mle
LaurenceKuhl Nov 7, 2023
d5c59ab
run black
mirpedrol Nov 7, 2023
4930690
fix left-padding spaces
mirpedrol Nov 7, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,9 +9,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- Template update v2.9 ([#52](https://github.com/nf-core/crisprseq/pull/52))
- Use `Channel.fromSamplesheet()` from `nf-validation` to validate input sample sheets and create an input channel ([#58](https://github.com/nf-core/crisprseq/pull/58))
- BAGEL2 as a module which detects gene essentiality
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### Fixed

- Change to `process_high` for the mageck mle module
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### Deprecated

## [v2.0.0 - Paprika Lovelace](https://github.com/nf-core/crisprseq/releases/tag/2.0.0) - [05.07.2023]
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