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NBISweden
/
pipelines-nextflow
A set of workflows written in Nextflow for Genome Annotation.
GNU General Public License v3.0
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Add citation.cff to allow citation.
#62
mahesh-panchal
closed
2 years ago
0
Update multiqc
#61
mahesh-panchal
closed
3 years ago
0
error TranscriptAssembly.nf with fastp
#60
LucileSol
closed
3 years ago
8
Add default time for Uppmax processes
#59
mahesh-panchal
closed
3 years ago
0
“Time Limit” error when running FunctionalAnnotation.nf on vertebrate scale genome
#58
fmsangdehi
closed
2 years ago
11
Augustus training parameter tuning
#57
royfrancis
closed
9 months ago
3
Patch interproscan. Disable container, use Uppmax module / conda env.
#56
mahesh-panchal
closed
3 years ago
1
[BUG] FunctionalAnnotation: InterProScan not working on Rackham with original configuration
#55
verku
closed
3 years ago
4
Quick link fix
#54
mahesh-panchal
closed
3 years ago
0
Add maintainer info to front page.
#53
mahesh-panchal
closed
3 years ago
1
update version of busco from v4 to v5 for the pipeline AnnotationPrep…
#52
LucileSol
closed
3 years ago
0
update version of gaas and agat in conda and singularity profile of all nextflow pipeline
#51
LucileSol
closed
3 years ago
1
AED filter not working?
#50
ViriatoII
closed
9 months ago
9
Conda env create fails (limited internet connection)
#49
ViriatoII
closed
3 years ago
4
Specify python3.7 for interproscan
#48
pontus
closed
3 years ago
0
Include maximum times for slurm jobs. Required on Uppmax.
#47
verku
closed
4 years ago
1
Add actions
#46
mahesh-panchal
closed
4 years ago
0
CI testing: Conda environment creation failed inside actions VM.
#45
mahesh-panchal
closed
9 months ago
1
CI testing: `.command.trace` file unable to be written from dockerised busco process
#44
mahesh-panchal
closed
4 years ago
1
agat version updated to 0.4.0, agat_sp_split_by_level2_feature.pl rep…
#43
royfrancis
closed
4 years ago
3
Update AGAT to version 0.4.0
#42
Juke34
closed
4 years ago
1
Update test profile parameters
#41
mahesh-panchal
closed
4 years ago
1
Test data for Abinitio training insufficient.
#40
mahesh-panchal
closed
4 years ago
8
Add emit statements
#39
mahesh-panchal
closed
4 years ago
2
Error: Session aborted -- Cause: Cannot emit a multi-channel output
#38
royfrancis
closed
4 years ago
0
Add Sample Sheet input to help process files
#37
mahesh-panchal
closed
9 months ago
1
Busco patch
#36
mahesh-panchal
closed
4 years ago
0
[New pipeline] EvidenceAlignment
#35
Juke34
opened
4 years ago
0
[New pipeline] MAKER3
#34
Juke34
opened
4 years ago
0
[New pipeline] RepeatMaskMyGenome
#33
Juke34
opened
4 years ago
0
[New pipeline] DeNovoRepeatLib
#32
Juke34
opened
4 years ago
0
[New pipeline] PASA
#31
Juke34
opened
4 years ago
0
[New pipeline] AnnotationToENA
#30
Juke34
opened
4 years ago
0
PBS script not loading conda
#29
ViriatoII
closed
4 years ago
1
Pb with running busco with AnnotationPreprocessing and Singularity
#28
LucileSol
closed
4 years ago
2
Update annotation preprocessing
#27
Juke34
closed
4 years ago
0
Add MultiQC to Annotation Preprocessing pipeline
#26
mahesh-panchal
opened
4 years ago
0
Abinitio outputs - Augustus
#25
ViriatoII
closed
4 years ago
2
Can't select 0.0 nor 0.00 in model_selection_value in AbinitioTraining.nf
#24
LucileSol
closed
4 years ago
11
Add fix for tsv output
#23
mahesh-panchal
closed
4 years ago
0
Merged TSVs missing from functional annotation output
#22
mahesh-panchal
closed
4 years ago
1
Annotation preprocessing, remove seqtk step
#21
Juke34
closed
4 years ago
0
step filter_by_locus_distance was unless because no value was set. No…
#20
Juke34
closed
4 years ago
0
Config file mandatory?
#19
ViriatoII
closed
4 years ago
11
Create subworkflow outputs
#18
mahesh-panchal
closed
4 years ago
2
Integrating workflows into a single workflow
#17
mahesh-panchal
opened
4 years ago
4
HiSat2 image for TranscriptAssembly workflow needs authentication token.
#16
mahesh-panchal
closed
4 years ago
1
update FunctionalAnnotation
#15
Juke34
closed
4 years ago
2
Add snap training
#14
mahesh-panchal
closed
4 years ago
0
Parameters and paths for test profile
#13
mahesh-panchal
closed
9 months ago
17
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