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UPHL-BioNGS
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Cecret
Reference-based consensus creation
MIT License
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26
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Does not parse pangolin file correctly
#71
erinyoung
closed
2 years ago
0
Issue setting maxcpus with v.2.0.2021115
#70
keckstrom
closed
2 years ago
4
Erin dev
#69
erinyoung
closed
2 years ago
0
fixed how paired end fastq files are read in
#68
erinyoung
closed
2 years ago
0
Adjust defaults to artic V4 primers
#67
erinyoung
closed
2 years ago
4
fastp and samtools versions look ... weird
#66
erinyoung
closed
2 years ago
0
Major Update
#65
erinyoung
closed
2 years ago
0
Nextclade needs an update
#64
erinyoung
closed
2 years ago
1
Updates to prepare for StaPH-B ToolKit V2
#63
k-florek
closed
2 years ago
4
No way to tell "trimmer" in summary file
#62
erinyoung
closed
2 years ago
1
Add option to bypass trimming
#61
erinyoung
closed
2 years ago
1
Error executing process > 'fastqc (12)'
#60
mramirezs
closed
2 years ago
5
added vadr parameter and upgraded to iqtree2
#59
erinyoung
closed
3 years ago
0
Fix DAG image of Cecret
#58
erinyoung
closed
3 years ago
0
for testing
#57
erinyoung
closed
3 years ago
0
Update Cecret on StaphB toolkit
#56
erinyoung
closed
3 years ago
1
Update
#55
erinyoung
closed
3 years ago
0
error with single reads
#54
erinyoung
closed
3 years ago
0
Update readme for kraken2 database
#53
erinyoung
closed
3 years ago
0
Update iqtree to iqtree
#52
erinyoung
closed
3 years ago
0
require certificate
#51
erinyoung
closed
3 years ago
0
fixed version
#50
erinyoung
closed
3 years ago
0
updated vadr and nextclade
#49
erinyoung
closed
3 years ago
1
Update nextclade container
#48
erinyoung
closed
3 years ago
1
config updates and bug fixes
#47
k-florek
closed
3 years ago
0
Erin dev
#46
erinyoung
closed
3 years ago
0
Erin dev
#45
erinyoung
closed
3 years ago
0
Quoting the clade name prevents a broken downstream summary.csv file
#44
molecules
closed
3 years ago
2
Erin dev
#43
erinyoung
closed
3 years ago
0
Updates to user configuration file
#42
k-florek
closed
3 years ago
3
change summary file to be more flexible with pangolin updates
#41
erinyoung
closed
3 years ago
0
Fix stageinmode
#40
erinyoung
closed
3 years ago
0
Count bases with > 10X coverage
#39
erinyoung
closed
3 years ago
0
Parallelize `sort` process
#38
fanninpm
closed
3 years ago
5
Process `summary` input file name collision
#37
fanninpm
closed
3 years ago
3
fixed formatting errors
#36
erinyoung
closed
3 years ago
0
added vadr and samtools plot-ampliconstats
#35
erinyoung
closed
3 years ago
0
added file back in
#34
erinyoung
closed
3 years ago
0
Erin dev
#33
erinyoung
closed
3 years ago
0
Retry block to address issue#31
#32
k-florek
closed
3 years ago
0
Segmentation fault for iVar variants process
#31
k-florek
closed
3 years ago
1
bedtools multicov overlap threshold is too low
#30
jgarbe256
closed
3 years ago
4
segmentation fault at ivar trim step
#29
vangalamaheshh
closed
3 years ago
6
Test run ...
#28
vangalamaheshh
closed
3 years ago
2
Feature Request : samtools fixmate when using ivar trim and samtools amplicon stats
#27
erinyoung
closed
2 years ago
1
Feature request : Insert Size
#26
erinyoung
closed
3 years ago
0
Feature Request : Amplicon bedfile
#25
erinyoung
closed
3 years ago
0
Create LICENSE
#24
erinyoung
closed
3 years ago
0
fixed gisaid fasta error
#23
erinyoung
closed
3 years ago
0
Erin dev
#22
erinyoung
closed
3 years ago
0
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