ellisrichardj BovTB-nf issues

ellisrichardj / BovTB-nf

Nextflow script for processing WGS data

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Fix id non bovis

#27 ellisrichardj closed 2 years ago
0
Fix inclusivity test

#26 ellisrichardj closed 3 years ago
1
Low qual flag

#25 ellisrichardj closed 3 years ago
0
Reduce failures for contaminated samples

#24 ellisrichardj opened 3 years ago
0
Restrict memory usage of AssignClusterCSS process

#23 ellisrichardj closed 3 years ago
1
Circleci project setup

#22 afishman closed 3 years ago
0
Dockerfile

#21 afishman closed 3 years ago
0
Using --lowmem option causes kraken2 to fail

#20 ellisrichardj closed 4 years ago
2
Formatting of BovPos.tsv output needs correcting

#19 ellisrichardj closed 4 years ago
0
Output table of snps for each sample

#18 ellisrichardj closed 4 years ago
3
Reliably detect M.bovis when it's at low prevalence in the sample

#17 ellisrichardj opened 4 years ago
3
[WIP] Matt edits

#16 MattoElGato closed 4 years ago
1
Test var call

#15 ellisrichardj closed 4 years ago
0
Test var call

#14 ellisrichardj closed 4 years ago
0
Bcftools consensus outputs reference base when data is missing

#13 ellisrichardj closed 4 years ago
0
Add process to ID samples that are not M. bovis

#12 ellisrichardj closed 5 years ago
1
Add explanations to output for failure to assign WGS Cluster

#11 ellisrichardj closed 4 years ago
2
Error in SNPfiltAnnot process

#10 ellisrichardj closed 5 years ago
1
VCF2Consensus process fails for some samples

#9 ellisrichardj closed 4 years ago
7
Update pipeline to use most recent version of M. bovis reference genome (LT708304)

#8 ellisrichardj closed 5 years ago
1
Update spoligotyping module to use standard names for spoligotypes

#7 ellisrichardj closed 5 years ago
2
Update Readme

#6 ellisrichardj opened 5 years ago
0
Infer phlogenetic cluster in addition to genotype

#5 ellisrichardj closed 5 years ago
1
Add run name to allow differentiation of the same sample sequenced multiple times

#4 ellisrichardj closed 4 years ago
0
Python script read stdin

#3 ellisrichardj closed 5 years ago
0
Genotype inference

#2 ellisrichardj closed 5 years ago
2
Update trimmomatic version

#1 ellisrichardj closed 5 years ago
0