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connor-lab
/
ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Executions fails because Nextflow preview function is deprecated
#134
alethomas
opened
6 months ago
0
Nanopore update
#133
JD2112
closed
10 months ago
0
Update config
#132
sofstam
closed
11 months ago
0
Update Syntax for Compatibility with Nextflow 23.04.4
#131
eptroendle
opened
11 months ago
0
Update nextclade 2.11
#130
sofstam
closed
1 year ago
0
Add nextflow dependency
#129
pdp10
opened
1 year ago
0
Fix dsl2 syntax errors
#128
rdeborja
opened
1 year ago
1
Sc2reporter comp
#127
LordRust
closed
2 years ago
1
Enable medaka to run V4 primer scheme
#126
pdp10
opened
2 years ago
0
Enable medaka to run V4 primer scheme
#125
pdp10
closed
2 years ago
0
Run versions process with nanopore medaka
#124
henningonsbring
closed
2 years ago
1
Update pangolin container
#123
sofstam
closed
2 years ago
0
Downgrade nextclade
#122
henningonsbring
closed
2 years ago
1
Fixing git aln2typeversion
#121
JezSw
closed
2 years ago
0
Update dockerfile
#120
sofstam
closed
2 years ago
0
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#119
thomasbtf
opened
2 years ago
0
fix: update to artic 1.2.2
#118
thomasbtf
opened
2 years ago
0
A new release for this pipeline ?
#117
valentinelsra
opened
2 years ago
2
Pin pip version in environment.yml
#116
MattBashton
opened
2 years ago
0
Completeness field to report JSON
#115
bede
closed
2 years ago
1
Adding nCoV-2019.primer.bed for analysis with midnight primer scheme
#114
henningonsbring
closed
2 years ago
1
uploaded dag
#113
JD2112
closed
2 years ago
0
Added channel_priority help
#112
BioWilko
closed
2 years ago
0
readgroup not found in provided primer scheme (1) for V4 scheme
#111
esha-joshi
opened
3 years ago
5
GFF included repo doesn't include ORF1ab frameshift
#110
tnguyensanger
opened
3 years ago
0
Add github action to build a Docker image and update for Nextflow 21.04.1
#109
antunderwood
opened
3 years ago
0
Guppyplex step not working
#108
KevinMenden
closed
3 years ago
0
nextclade added to the pipeline
#107
JD2112
closed
3 years ago
0
Medaka sp3
#106
nick297
closed
3 years ago
0
New protocolo Nanopore V1200
#105
ghost
opened
3 years ago
0
Unparseable date error
#104
wtmatlock
opened
3 years ago
1
variants with low SupportFraction change the sequence
#103
paraslonic
opened
3 years ago
0
Snakemake file
#102
ksw9
opened
3 years ago
1
Variant definitions
#101
m-bull
opened
3 years ago
0
Illumina
#100
dianalir
opened
3 years ago
0
Fix params.gff undefined and remove CLIMB upload
#99
m-bull
closed
3 years ago
0
Accidental pull request. Ignore me.
#98
sylvinite
closed
3 years ago
0
Nanopore-conda-environment.yaml update
#97
tarah28
opened
3 years ago
0
Failed samples
#96
gdauria
opened
3 years ago
0
docker profile not working
#95
rrdavis77
opened
3 years ago
3
Access to undefined parameter 'gff'
#94
hodeco
opened
3 years ago
2
Using the pipeline for non-artic primers?!
#93
ahmedmagds
closed
3 years ago
2
Frameshift variants may interfere with typing in type_vcf.py, even with low ALT_FREQ
#92
dfornika
opened
3 years ago
7
Handle variants with consequence type 'stop_retained' as synonymous variants.
#91
dfornika
closed
3 years ago
0
type_vcf.py doesn't handle variants with consequence 'stop_retained'
#90
dfornika
closed
3 years ago
0
Make QC cutoffs configurable, but with sensible defaults
#89
m-bull
opened
3 years ago
0
Add --force-no-qc flag
#88
m-bull
opened
3 years ago
0
Sample names inherit part of illumina's nomenclature for index and lane
#87
MattBashton
opened
3 years ago
0
Error: prepareReferenceFiles
#86
yockping
opened
3 years ago
4
Update documentation
#85
m-bull
opened
3 years ago
0
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