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jaleezyy
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covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
MIT License
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Patch 1.6.4
#142
jaleezyy
closed
3 months ago
0
Artic-ncov2019 primer scheme V5.3.2
#141
ReemaSingh
closed
5 months ago
3
Dependency issues on new install with ivar conda environment
#140
dgaston
closed
6 months ago
5
Nextclade v3 Support
#139
jaleezyy
closed
8 months ago
0
Pipeline fails at run_lineage_assignment when trying to use Nextclade version 3.0.0
#138
PierreLyons
closed
8 months ago
4
gunzip silently fails when running get_data_dependencies.sh
#137
dgaston-nsh
opened
1 year ago
1
Better handle failing samples, add per-rule installation, and general updates
#136
jaleezyy
closed
1 year ago
0
Lineage assignment dependency adjustment
#135
jaleezyy
closed
1 year ago
0
Quality of Life changes
#134
jaleezyy
closed
1 year ago
0
Update lineage assignment dependency
#133
jaleezyy
closed
1 year ago
0
Patch nextclade v2+ compatibility
#132
jaleezyy
closed
2 years ago
0
Continued ncov-tools and pangolin support
#131
jaleezyy
closed
2 years ago
0
Update to 1.5.4
#130
DarianHole
closed
2 years ago
1
Update nextclade and pangolin toggle
#129
jaleezyy
closed
2 years ago
0
Update SIGNAL for Pangolin v4.0+ compatibility
#128
jaleezyy
closed
2 years ago
0
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#127
thomasbtf
closed
2 years ago
2
SIGNAL lineage assignment versioning; ncov-tools integration
#126
jaleezyy
closed
2 years ago
0
Update npm nextclade to the proper nextclade_cli
#125
fmaguire
closed
2 years ago
1
RuleException in line 549 of: filepath/Snakefile: 'Params' object has no attribute 'unlabelled_output_dir'
#124
christinehehnly
closed
2 years ago
2
Cleanup
#123
jaleezyy
opened
2 years ago
0
Support IonTorrent .bam input
#122
fmaguire
opened
3 years ago
0
Galaxy workflow?
#121
domenico-simone
opened
3 years ago
0
Incorporate scorpio calls into report
#120
fmaguire
opened
3 years ago
0
ValidationError: 'sample' is a required property
#119
Lukas-Vasionis
closed
3 years ago
2
support for pangolin v3.0.1
#118
SupriseCestEric
closed
3 years ago
2
Convert rules for wrapped tools to official wrapper
#117
fmaguire
opened
3 years ago
0
Fix containerization
#116
fmaguire
opened
3 years ago
0
Add Continuous Integration tests and linting
#115
fmaguire
opened
3 years ago
0
Revisit output layout
#114
fmaguire
opened
3 years ago
0
Primer Scheme Correction
#113
moreiradaniel
closed
3 years ago
1
Switch remaining default output to freebayes vs iVar
#112
fmaguire
opened
3 years ago
0
Lineage Assignment Failure preventing postprocess
#111
christinehehnly
closed
3 years ago
1
Pangolin Update changes probability column to conflict breaking assign_lineages.py
#110
DarianHole
closed
3 years ago
1
Add quick alignment and updates to postprocess reporting
#109
jaleezyy
closed
3 years ago
0
Add lineage assignments to summary table
#108
fmaguire
closed
3 years ago
1
Compare freebayes/ivar consensus directly
#107
fmaguire
closed
3 years ago
2
Add FreeBayes variant calling and restore multiple pool sample support
#106
jaleezyy
closed
3 years ago
0
Error during host removal
#105
kdmack87
closed
3 years ago
1
Error when download data dependencies with docker image
#104
domenico-simone
closed
3 years ago
1
Clade assignment
#103
fmaguire
closed
3 years ago
1
Merge latest dev updates to master
#102
fmaguire
closed
3 years ago
0
Add test
#101
fmaguire
closed
3 years ago
0
Remove rule due to unpairing issue for some users
#100
fmaguire
closed
3 years ago
2
Add Nasir et al citation to repo README
#99
agmcarthur
closed
3 years ago
0
Kraken2 utility
#98
fmaguire
closed
2 years ago
3
Update ncov-tools integration with SIGNAL
#97
jaleezyy
closed
2 years ago
5
Fail early if CONDA_EXEC is not set
#96
pvanheus
closed
4 years ago
1
Oicr param update
#95
fmaguire
closed
4 years ago
1
Update params in-line with OICR workflow
#94
fmaguire
closed
4 years ago
0
Merge read pairs
#93
atduggan
opened
4 years ago
0
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