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poreCov
SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Singularity container execution of pangolin crashes with recent nextflow versions
#272
Krannich479
opened
1 month ago
6
[Question] CI for Variant Calling
#271
Krannich479
opened
1 month ago
5
Test Freyja Update function
#270
hoelzer
opened
1 month ago
11
added the latest midnight primers (V5.2.0_1200)
#269
MarieLataretu
opened
1 month ago
2
Freyja integration
#268
DataSpott
closed
1 month ago
7
Update medaka to get the latest models
#267
MarieLataretu
opened
2 months ago
1
Publish VCF files
#266
hoelzer
opened
3 months ago
2
changed the error strategy in slurm profile
#265
MarieLataretu
closed
1 month ago
0
bump default container version for pangolin and nextclade
#264
MarieLataretu
closed
4 months ago
5
Process retry in slurm profile
#263
MarieLataretu
closed
1 month ago
1
CovarPlot fails w/ custom BED
#262
hoelzer
closed
4 months ago
5
Feature: add nextclades pango assigment
#261
MarieLataretu
closed
5 months ago
2
new pangolin table columns
#260
replikation
closed
5 months ago
1
The pipeline fails in artic_ncov_wf_artic_medaka
#259
Bioloko
closed
8 months ago
7
fixed disabling of artic normalisation
#258
MarieLataretu
closed
9 months ago
1
added timestamp to reports; solves #256
#257
MarieLataretu
closed
7 months ago
0
Warning when execution report and timeline already exists
#256
MarieLataretu
closed
5 months ago
1
Update medaka
#255
MarieLataretu
closed
1 year ago
0
MinKNOW/Guppy update needs new model for R10.4.1 5 kHz
#254
hoelzer
closed
1 year ago
6
updated president version and docker hub account
#253
MarieLataretu
closed
1 year ago
1
[Enhancment] publish more logs/intermediate files from ARTIC
#252
MarieLataretu
closed
11 months ago
0
[Feature] added parameter artic_normalize
#251
MarieLataretu
closed
11 months ago
0
Update medaka in artic
#250
hoelzer
closed
1 year ago
7
Added new version of V1200 primer-set, changing old V1200 to V1200_or…
#249
DataSpott
closed
1 year ago
0
Update --help to list up-to-date primer schemes that are supported
#248
hoelzer
closed
1 year ago
0
Update Medaka to support R10.4.1 models
#247
hoelzer
closed
1 year ago
14
VarSkipV2b primer does not work as expected
#246
svonoy
closed
1 year ago
7
publish primersitereport from medaka output
#245
MarieLataretu
closed
11 months ago
0
bumped predefined LCS table to 2023-01-26
#244
MarieLataretu
closed
1 year ago
1
[Feature] more info on Ns
#243
MarieLataretu
closed
1 year ago
3
[Feature] add ARTIC V5 and V5.1
#242
MarieLataretu
closed
1 year ago
3
summary_report.py fails
#241
MarieLataretu
closed
1 year ago
7
Medaka step fails in the -profile fastq_test
#240
hoelzer
closed
1 year ago
3
Split fasta improvement
#239
DataSpott
closed
1 year ago
2
Add new V5 ARTIC primer BED
#238
hoelzer
closed
1 year ago
5
adds VSS2b
#237
bwlang
closed
1 year ago
1
Only calculate NanoPlot after read filtering step
#236
hoelzer
closed
1 year ago
5
added skip-scorpio parameter fixes #234
#235
MarieLataretu
closed
2 years ago
13
add skip scorpio parameter to pangolin
#234
MarieLataretu
closed
2 years ago
1
publish vcf file, fixes #232
#233
MarieLataretu
closed
2 years ago
0
export variant file (vcf)
#232
oliverdrechsel
closed
2 years ago
1
LCS UCSC marker update feature
#231
MarieLataretu
closed
2 years ago
12
Workflow failed at artic_medaka, no '2.Genomes' output, with test_fastq and actual sample
#230
Krysasp
closed
2 years ago
1
"split-fasta"-process fails due to leading empty line
#229
DataSpott
closed
1 year ago
0
Release1.5
#228
replikation
closed
2 years ago
2
Frameshift correction
#227
hoelzer
opened
2 years ago
0
Private mutation from nextclade
#226
MarieLataretu
opened
2 years ago
1
Split LCS barplot
#225
MarieLataretu
closed
2 years ago
1
Pangolin4 update
#224
RaverJay
closed
2 years ago
12
Runs fail at barcode22
#223
JaMaack
closed
2 years ago
8
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