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cbg-ethz
/
V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
https://cbg-ethz.github.io/V-pipe/
Apache License 2.0
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Updated benchmark
#156
LaraFuhrmann
closed
4 weeks ago
2
improve tutorial_0_install.md
#155
prajwalkulkarni
opened
2 months ago
2
Add issue templates
#154
prajwalkulkarni
opened
2 months ago
1
Installation Doc Update
#153
hrishikeshh
opened
2 months ago
0
Snakemake workflow catalog standardized usage
#152
uniqueg
closed
1 month ago
0
Snakemake standardized usage
#151
uniqueg
closed
1 month ago
0
adding viloca to the workflow
#150
LaraFuhrmann
closed
4 weeks ago
5
Add virus configs
#149
LaraFuhrmann
closed
1 month ago
3
Problem in the deconvolution step
#148
Xuyen21
opened
5 months ago
4
Snakemake dry run 404
#147
helmotw
closed
8 months ago
9
Activating snv in sars tutorial leads to error
#146
schlaepferp
opened
1 year ago
2
vpipe broken? ModuleNotFoundError: No module named 'pandas'
#145
schlaepferp
closed
1 year ago
2
included lofreq in master snake file
#144
mcarrara-bioinfo
closed
1 year ago
1
add minimap2 aligner
#143
DrYak
closed
1 year ago
0
PredictHaplo fix ouput directory
#142
DrYak
closed
1 year ago
1
[Add] monkeypox config + resources
#141
LaraFuhrmann
closed
1 year ago
3
Fix diversity measures
#140
LaraFuhrmann
closed
1 year ago
1
Missing input files for rule generate_web_visualization
#139
carlottaolivero
opened
1 year ago
0
Error in rule hmm_align: HIV in Vpipe
#138
vfdiamante
opened
1 year ago
2
hiv-tutorial fails with haplotype_reconstruction: savage, and SAVAGE command output is dumped into terminal instead of log
#137
Masterxilo
opened
1 year ago
0
hiv-tutorial works with haploclique, but fails with predicthaplo
#136
Masterxilo
opened
1 year ago
0
predicthaplo does not work on sars-cov-2 tutorial
#135
Masterxilo
closed
1 year ago
1
[UX issue] multiple GFF
#134
DrYak
opened
1 year ago
1
[UX issue] unknown keywords in config file
#133
DrYak
opened
1 year ago
1
frameshift_deletion_checks, simBench & Haplotype callers
#132
dimitris-karapliafis
closed
1 year ago
6
Feature tutorial - pull new tutorial with example data to master branch
#131
LaraFuhrmann
closed
1 year ago
1
[fix] populatin_nucleotide_diversity
#130
LaraFuhrmann
closed
1 year ago
3
[fix] population nucleotide diverstiy: corrected handling for multiple variants at same position.
#129
LaraFuhrmann
closed
2 years ago
2
fix #127
#128
LaraFuhrmann
closed
1 year ago
4
Conflict in quality_assurance.smk with custom datadir-path
#127
LaraFuhrmann
closed
1 year ago
0
Warning: All reads at position 4045 in the same reverse orientation ?
#126
Vinoy-UKHSA
opened
2 years ago
1
[FEAT] Added sftp sync staging
#125
mcarrara-bioinfo
closed
2 years ago
1
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#124
thomasbtf
opened
2 years ago
1
Rubicon
#123
DrYak
closed
2 years ago
1
please document haploclique.extra_parameters
#122
Masterxilo
opened
2 years ago
3
Allow passing arbitrary parameters to haploclique invokation
#121
kpj
closed
2 years ago
1
Getting snake error
#120
dstcr
opened
2 years ago
23
Running with tutorial dataset giving all empty file
#119
wasimbt
opened
2 years ago
6
Pulling back rubicon into master
#118
DrYak
closed
2 years ago
1
Feature diversity measures
#117
LaraFuhrmann
closed
2 years ago
0
S3c sis task 7 and 11
#116
uweschmitt
closed
2 years ago
2
Quasispecies Reconstruction Benchmark
#115
kpj
closed
8 months ago
7
wrong url for release download in quick install
#114
Masterxilo
closed
2 years ago
2
BAM trimming according to primers with ivar, new rule
#113
michalogit
closed
1 year ago
3
Add phylogeny and read alignment visualisation
#112
monicadragan
closed
2 years ago
1
Add MegaLinter GA workflow
#111
kpj
closed
2 years ago
2
Restructure V-pipe tutorials and website
#110
kpj
closed
2 years ago
0
S3c sis task 7
#109
uweschmitt
closed
2 years ago
1
S3C-SIS-TASK-11: Consensus sequences need to be manually imported.
#108
uweschmitt
closed
2 years ago
1
The order of jobs does not reflect the order of execution. Any help?
#107
carlottaolivero
opened
2 years ago
1
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