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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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Pangolin container not updated
#87
sofstam
opened
4 months ago
0
Update ivar to avoid frame shift issues
#86
talnor
opened
6 months ago
0
add java mem options
#85
talnor
closed
5 months ago
1
nanopore container splits
#84
JD2112
opened
8 months ago
2
Draft PR for the course
#83
sofstam
opened
9 months ago
0
Add pycoQC docker to GMS-Artic and Dockerhub
#82
talnor
opened
9 months ago
1
Move pangolin-data out of docker image
#81
talnor
opened
9 months ago
0
Fix GitHub workflow docker builds
#80
talnor
closed
9 months ago
2
Docker build bug
#79
talnor
closed
9 months ago
0
medaka workflow fails at bcftools
#78
fwa93
opened
1 year ago
0
medaka worflow fails if you have few reads
#77
fwa93
opened
1 year ago
1
Include all python3 versions
#76
sofstam
closed
1 year ago
3
Black test
#75
sofstam
closed
1 year ago
0
Update nextclade
#74
sofstam
closed
9 months ago
5
Rich set to fixed version
#73
sofstam
closed
1 year ago
3
--scheme midnight-primer/V1/ gives an error
#72
fwa93
closed
1 year ago
1
Revert "Update nextclade"
#71
JD2112
closed
1 year ago
0
Update nextclade
#70
sofstam
closed
1 year ago
7
Have the possibility to add a reference sequence as root for nextclade
#69
pbiology
opened
1 year ago
1
Update nextclade to latest >= 2.7.0
#68
pbiology
closed
1 year ago
1
minor fix: go_fasta version
#67
JD2112
closed
1 year ago
0
Workflows need to be updated for NextFlow=>22
#66
JD2112
closed
9 months ago
0
Pangolin container separated from Illumina and Nanopore workflows
#65
JD2112
closed
1 year ago
18
Build new nanopore container
#64
sofstam
closed
1 year ago
0
Multiqc medaka
#63
henningonsbring
closed
1 year ago
6
Run versions process with nanopore medaka workflow
#62
henningonsbring
closed
1 year ago
3
Update pangolin container
#61
sofstam
closed
1 year ago
2
Specify pangolin version via variable at docker build
#60
dodslaser
closed
1 year ago
1
Use conda to solve environment instead of mamba
#59
sofstam
closed
2 years ago
3
Fix mamba
#58
sofstam
closed
2 years ago
0
Update Dockerfile
#57
henningonsbring
closed
2 years ago
10
downgraded nextclade
#56
henningonsbring
closed
2 years ago
1
Update dockerfile
#55
sofstam
closed
2 years ago
1
Muscle needs to be downgraded for nanopore analyses
#54
henningonsbring
closed
2 years ago
3
Update pangolin v4
#53
talnor
closed
2 years ago
3
Updates for pangolin v.4.0
#52
talnor
closed
2 years ago
3
Update illumina.config
#51
JD2112
closed
2 years ago
0
Nanopore requires --scheme to run the pipeline
#50
sofstam
opened
2 years ago
0
Revert "Primer scheme"
#49
JD2112
closed
2 years ago
0
Primer scheme
#48
JD2112
closed
2 years ago
4
Muscle version 3.8 to allow nanopore analysis with medaka
#47
henningonsbring
closed
2 years ago
1
The CLI option --scheme-directory does nothing
#46
sylvinite
closed
2 years ago
2
Update the local singularity containers every second week
#45
sofstam
closed
2 years ago
4
Adding *primer.bed file for midnight primer scheme
#44
henningonsbring
closed
2 years ago
0
Nextclade latest
#43
sofstam
closed
2 years ago
0
Add software version scrape
#42
talnor
closed
2 years ago
0
Update of nextclade in the environment file for Illumina and Nanopore
#41
sofstam
closed
2 years ago
1
Update dockerfile for nanopore
#40
sofstam
closed
2 years ago
0
Clean human reads before initialisation
#39
pbiology
opened
2 years ago
4
clone master branch to main
#38
JD2112
closed
2 years ago
2
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