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Added liftoff, integrated with pfr/nxf-modules, and some minor improvements #2

Merged
merged 59 commits into from
Jan 11, 2024
Merged

Added liftoff, integrated with pfr/nxf-modules, and some minor improvements #2

merged 59 commits into from
Jan 11, 2024

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GallVp
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@GallVp GallVp commented Jan 10, 2024

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@GallVp GallVp force-pushed the dev branch 3 times, most recently from fc2856b to 8f065a5 Compare January 11, 2024 00:38
GallVp added 27 commits January 11, 2024 13:41
@GallVp
Added updated info about nf-core modules
ee9d0b9
@GallVp
Turned off SortMeRNA by default
7f03697
@GallVp
Decouple target assemblies and read qc/align
232493a
@GallVp
A bit of reformatiing
4f2ed8e
@GallVp
Started implementing liftoff
8b83c61
@GallVp
Checkpoint before major reshuffle
37ce74e
@GallVp
Reformatted local modules
d148f18
@GallVp
Now using galaxy containers
e63e22f
@GallVp
Extracted some subworkflows
1978308
@GallVp
Extracted a few subworkflows
10a0158
@GallVp
Extracted subworkflows uptill BRAKER3
2031790
@GallVp
Inc liftoff
f315467
@GallVp
Added polished out channel to liftoff
f10ae94
@GallVp
Added gffread before liftoff
80db270
@GallVp
Updated flowchart
bb9b8b0
@GallVp
Added liftoff options
c982946
@GallVp
Started moving to nf-core/tools
c8ff8da
@GallVp
Reimported modules using nf-core/tools
f285461
@GallVp
Reimported kherronism modules with nf-core/tools
bea59ef
@GallVp
Updated braker3
2dda752
@GallVp
Updated repeatmasker
8efa34d
@GallVp
Updated modules
8d31976
@GallVp
Imported fastavalidate and liftoff from pfr/nxf-modules
5eaa87b
@GallVp
Updated modules and subworkflows
0a96c7f
@GallVp
Added EDTA from pfr/nxf-modules
8a6c5fe
@GallVp
Updated config
26c33fa
@GallVp
Integrated fastavalidator
9e58314
GallVp added 26 commits January 11, 2024 13:41
@GallVp
SORTMERNA now has stub
ac45bbb
@GallVp
Cleaned up prepare_assembly
ed6aa33
@GallVp
Cleaned up preprocess_rnaseq
144edb2
@GallVp
Reformatted and inc ALIGN_RNASEQ
a79c187
@GallVp
Cleaned up and inc PREPARE_EXT_PROTS
6f61f5d
@GallVp
Cleanedup BRAKER3
1184795
@GallVp
Updated fastp, sortmerna and liftoff
a9f1fc6
@GallVp
Cleaned up fasta_liftoff
d0faf8d
@GallVp
Updated fasta_edta_lai
27a1293
@GallVp
Added script for local stub run
3867ed5
@GallVp
Samplesheet now accepts relative paths
4761491
@GallVp
Updated modules
8ced027
@GallVp
Removed -exclude_partial and updated flowchart
fce65a0
@GallVp
Separated test config for local and pfr
582f3fa
@GallVp
Fixed local script typo
e213bd3
@GallVp
Fixed apptainer scope bug in base config
c961ab0
@GallVp
Updated README
260c706
@GallVp
Readded -exclude_partial and now using teambraker container
565e7d7
@GallVp
Added config for test data and quay.io container for braker3
47b7c40
@GallVp
Now using repeatmodeler by default
664fba1
@GallVp
BRAKER3 now runnable with test data
dea4bb5
@GallVp
Added editor config
0535b1a
@GallVp
Disabled sortmerna by default added option to save cat bam
457a643
@GallVp
Added pre-commit
784bb54
@GallVp
Updated manifest
a4ada59
@GallVp
Fixed linting errors
4de72ab
@GallVp GallVp merged commit fd9c0ac into main Jan 11, 2024
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@GallVp GallVp deleted the dev branch January 11, 2024 01:26
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@GallVp