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genomic-medicine-sweden
/
gms-artic
A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Rename files before upload to AWS nodes
#37
pbiology
opened
2 years ago
0
Pangolin typing with medaka
#36
henningonsbring
closed
2 years ago
0
GHactions 37d2b7a
#35
sofstam
closed
2 years ago
2
Add GHaction
#34
sofstam
closed
2 years ago
0
Update nextflow version in pull_request.yml
#33
sofstam
closed
2 years ago
2
Handle versioning of gms-artic
#32
sofstam
opened
2 years ago
1
Fix bug for many samples
#31
talnor
closed
2 years ago
0
Test GHaction on PR
#30
sofstam
closed
2 years ago
1
GHactions
#29
sofstam
closed
2 years ago
1
Update docker image container and nextflow config
#28
JD2112
closed
2 years ago
0
Added label and tags for qc
#27
talnor
closed
2 years ago
1
update workflow-images with pipelines DAG
#26
JD2112
closed
2 years ago
0
Fix insertsize catch
#25
talnor
closed
2 years ago
1
Sample input should be from list
#24
pbiology
closed
2 years ago
0
Skip control samples for uploads
#23
pbiology
opened
2 years ago
0
Master branch should change name to main
#22
pbiology
opened
2 years ago
2
Midnight update
#21
JD2112
closed
2 years ago
0
Add QC metrics
#20
talnor
closed
2 years ago
0
Update to latest version of freebayes
#19
talnor
closed
2 years ago
0
Fix permissions for scripts
#18
talnor
closed
2 years ago
0
Updates and new additions
#17
JD2112
closed
3 years ago
1
Remove duplicate dependency
#16
talnor
closed
3 years ago
0
Jd2112 nextclade
#15
JD2112
closed
3 years ago
1
Updated pangolin installation
#14
talnor
closed
3 years ago
0
updated pangolin and dockerhub
#13
JD2112
closed
3 years ago
3
Add mem params
#12
talnor
closed
3 years ago
0
Sync from upstream
#11
sylvinite
closed
3 years ago
0
Collate pangolin output
#10
pbiology
closed
2 years ago
2
Sge executor
#9
pbiology
closed
3 years ago
1
Minor cleanup
#8
sylvinite
closed
3 years ago
0
Add multiqc
#7
sylvinite
closed
3 years ago
1
Run pangolin on concatinated consensus file
#6
sylvinite
closed
3 years ago
2
Site specific configurations
#5
pbiology
opened
3 years ago
2
Use GMS-Artic images through dockerhub
#4
sylvinite
closed
2 years ago
3
Handle insufficent resources for samtools mpileup
#3
sylvinite
opened
3 years ago
0
Add QC functions
#2
sylvinite
closed
3 years ago
1
Pangolin added to artic-nf
#1
JD2112
closed
3 years ago
0
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