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epi2me-labs
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wf-artic
ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Erreur on: nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 -- scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1100 --out_dir
#114
Yacsaw81
opened
2 weeks ago
0
Request to implement a Sunburst plot in the wf-artic report like the wf-metagenomics report
#113
mgurbano
opened
1 month ago
0
EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data"
#112
mgurbano
closed
1 month ago
5
Invalid output definition when I try to run test data
#111
MauriAndresMU1313
closed
4 months ago
2
Nextclade version hardcoded
#110
ammaraziz
closed
5 months ago
1
feat: allow use of latest nextclade v3 tree with v2 binary
#109
corneliusroemer
closed
7 months ago
0
Error with initial --help command
#108
kiranpatil222
closed
8 months ago
1
Nextclade v2 no longer maintained
#107
ammaraziz
closed
8 months ago
8
Fix HTML report output errors on int sample_names
#106
ammaraziz
closed
4 months ago
1
Add artic minion logging for debugging
#105
ammaraziz
closed
5 months ago
2
Medaka unable to download model
#104
ammaraziz
closed
5 months ago
3
Readme command is wrong for help
#103
doi-vid
closed
11 months ago
1
No nextclade.tsv output
#102
rgn3210
closed
11 months ago
0
ERROR ~ Error executing process > 'pipeline:report' when sample names are numbers only
#101
rrdavis77
closed
11 months ago
5
MacOS M1 chip, sed making tmp file with wrong permissions and failure to export issue
#100
rebeelouise
closed
1 year ago
5
errors from downloading epi2me wf
#99
devfidz
closed
1 year ago
1
Problems process pipeline:runArtic
#98
Bioloko
closed
1 year ago
10
Consensus sequences are not produced even after good coverage
#97
Rohit-Satyam
closed
1 year ago
5
Error updating Pangolin
#96
alexahess
closed
8 months ago
8
Adding support for dna_r10.4.1_e8.2_400bps_sup@v4.2.0
#95
llk578496
opened
1 year ago
6
Unable to pull from repository
#94
llk578496
closed
1 year ago
2
Primer dropout with a suspected XBB.1.1 sequence
#93
iahdb
closed
1 year ago
5
Option to output failed vcf
#92
ammaraziz
closed
1 year ago
1
test
#91
mattdmem
closed
1 year ago
1
Force datatype of str for column `sample_name`.
#90
ammaraziz
closed
1 year ago
1
Missing barcodes from sample input break the pipeline
#89
ammaraziz
closed
8 months ago
3
ERROR ~ Error executing process > 'pipeline:report (1)'
#88
Habibk91
closed
1 year ago
2
Why I am getting a Command Trace Error
#87
navyn007
closed
1 year ago
4
Why I am getting a Command Trace Error
#86
navyn007
closed
1 year ago
1
Inconsistent results
#85
phongphak
closed
1 year ago
2
pipeline:runArtic (1)'
#84
Habibk91
closed
1 year ago
2
[Bug]: Error executing process > 'pipeline:report (1)' when using sample_sheet
#83
davidbante
closed
1 year ago
3
[Bug]: WARNING due to undefined param.threads
#82
ammaraziz
closed
1 year ago
1
Question: Custom scheme Midnight-IDT/V2
#81
fwa93
closed
1 year ago
2
Artic V5.3.2 primer scheme
#80
VLeducq
closed
1 year ago
5
[Bug]: Error executing process > 'pipeline:report (1)'
#79
myorick
closed
1 year ago
1
[Bug]: Problem with a custom scheme
#78
michallaz
closed
1 year ago
1
[enhancement]: wf-artic for other viruses - skip nextclade and pangolin
#77
sarahryter
closed
1 year ago
3
[Bug]: epi2me-labs/wf-artic v0.3.22 EPI2ME Labs V4.1.2 workflow primer scheme selection
#76
PWSmit
closed
1 year ago
4
[Bug]: Has medaka models updated to support v14 chemistry
#75
llk578496
closed
1 year ago
3
[Bug]: publish output process refactoring recommended
#74
phyden
closed
1 year ago
1
[Bug]: wf-artic v0.3.21 on epi2melabs v4.0.0 looks for primer scheme in directory that doesn't exist
#73
kneubehl
closed
1 year ago
15
Enable overwrite of reports as required from nf v22.10.0
#72
corneliusroemer
closed
1 year ago
1
[Bug]: Error `Trace file already exists` when rerunning command after failure
#71
corneliusroemer
closed
1 year ago
2
[Bug]: sed: couldn't open temporary file ./sed3unqLx: Permission denied
#70
corneliusroemer
closed
1 year ago
2
Fix typo in README
#69
corneliusroemer
closed
1 year ago
0
Regarding filtering of Low Frequency and Subclonal Mutations
#68
Rohit-Satyam
closed
1 year ago
4
[Bug]: not really a bug... a question
#67
arielamadio
closed
1 year ago
0
[Bug]: FASTCAT command not found
#66
NHPttt
closed
1 year ago
1
[enhancement:] wf-artic pipeline filters too many reads
#65
Rohit-Satyam
closed
1 year ago
1
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