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jts
/
ncov-tools
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
47
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16
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Error on watch branch
#61
poquirion
closed
3 years ago
10
config file: making snp tree generation optional
#60
nknox
closed
3 years ago
7
Documentation for ncov-watch input
#59
dfornika
closed
3 years ago
3
Fix conda package name for parasail
#58
dfornika
closed
3 years ago
0
Conda package name for parasail is 'parasail-python'
#57
dfornika
closed
3 years ago
2
Change annotate variant rule
#56
rdeborja
closed
3 years ago
0
Add snpeff support
#55
rdeborja
closed
3 years ago
0
Removed parser package from repo, added pip install ncov-parser, includes PO PR 53
#54
rdeborja
closed
3 years ago
0
Image setup
#53
poquirion
closed
3 years ago
5
align2alleles.py will skip fixed variants when --min-allele-count is greater than 1
#52
jts
opened
3 years ago
0
Parser from master branch in github installed in dependecies installed
#51
poquirion
closed
3 years ago
2
added recurrent heatmap to rules
#50
rdeborja
closed
3 years ago
1
Singularity containerisation to enable use in conda-limited environments
#49
fmaguire
closed
3 years ago
4
One target to rule them all?
#48
andersgs
closed
3 years ago
3
Workflow structure
#47
andersgs
closed
3 years ago
6
added the creation of the aa heatmap to the end of the annovar workflow
#46
rdeborja
closed
3 years ago
0
Issue 44
#45
rdeborja
closed
3 years ago
0
Make the completeness threshold for including a sample in the tree-snp plot configurable
#44
jts
closed
3 years ago
1
Add annovar
#43
rdeborja
closed
3 years ago
0
Add aa mutation heatmap
#42
rdeborja
closed
3 years ago
0
pinned biopython to version 1.77
#41
rdeborja
closed
3 years ago
0
datafunk fails with biopython >1.77
#40
dfornika
closed
3 years ago
2
Install parser using environment.yml
#39
m-bull
closed
4 years ago
4
added the MIT license file
#38
rdeborja
closed
4 years ago
0
license?
#37
mcroxen
closed
4 years ago
3
Create amplicon coverage table
#36
rdeborja
closed
4 years ago
0
tmp_bam rule
#35
mcroxen
closed
3 years ago
4
Negative control samples and filenames
#34
rdeborja
closed
3 years ago
11
Add primer bed
#33
rdeborja
closed
4 years ago
0
updated get_metadata_file to pass {data_root} if used in config file
#32
rdeborja
closed
4 years ago
0
Generation of summary reports without inputting negative control names
#31
DarianHole
closed
4 years ago
3
Fix consensus variant pattern
#30
rdeborja
closed
4 years ago
0
Update README to include mamba install instructions
#29
fmaguire
closed
4 years ago
0
ncov-tools conda environment
#28
raphenya
closed
4 years ago
8
negative control check bed
#27
jts
closed
4 years ago
1
get_qc.py getting passed unrecognized argument --run_name
#26
DarianHole
closed
4 years ago
2
Fix negative num weeks issue
#25
rdeborja
closed
4 years ago
0
Add run name to qc summary
#24
rdeborja
closed
4 years ago
0
updated Snakefile to fix data_root but for qc rule
#23
rdeborja
closed
4 years ago
0
all_summary_qc fails if data_root not set to 'data'
#22
DarianHole
closed
4 years ago
3
Fix alleles snv count
#21
rdeborja
closed
4 years ago
0
added removal of suffix /ARTIC/nanopolish from nanopore alleles data
#20
rdeborja
closed
4 years ago
0
Remove num months
#19
rdeborja
closed
4 years ago
0
Fix ont vars flag
#18
rdeborja
closed
4 years ago
0
Updated readme
#17
rdeborja
closed
4 years ago
0
Merged ncov_parser into ncov-tools
#16
rdeborja
closed
4 years ago
0
Mixture check improvements
#15
jts
closed
4 years ago
0
Update environment for pangolin compatibility
#14
jaleezyy
closed
4 years ago
2
Issue 12 hardcoded filenames
#13
rdeborja
closed
4 years ago
0
Rule 'make_sample_qc_summary': Hard-coded filenames
#12
dfornika
closed
4 years ago
5
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