polio-nanopore piranha issues

polio-nanopore / piranha

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issues

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Error running wg analysis mode: cannot find WG snakefile (piranha_wg.smk)

#239 eduardoscopel opened 1 day ago
0
Not urgent - error running wg pipeline

#238 CatherineTroman opened 1 week ago
4
Fix Dockerfile

#237 rmcolq opened 1 week ago
1
Error during consensus building v1.2.3

#236 CatherineTroman opened 1 week ago
7
Semicolon as separator in barcodes.csv

#235 ebujaki opened 2 months ago
0
New install issue - Snakemake and PuLP conflict

#234 Desperate-Dan opened 2 months ago
1
Haplo issue

#233 ZoeVance closed 3 months ago
0
end extension by bam meddling? alt mapper either

#232 aineniamh opened 3 months ago
0
implement maskara for npevs

#231 aineniamh opened 3 months ago
0
Error when running haplotyping

#230 CatherineTroman closed 3 months ago
2
Ev reads present?

#229 Ceres90 opened 3 months ago
7
Bringing epi2me_debug up to date

#228 Desperate-Dan closed 3 months ago
0
Epi2me debug

#227 Desperate-Dan closed 3 months ago
0
Labels not visible on tree in report

#226 AShaw1802 opened 3 months ago
2
Rapid barcoding kit

#225 a-qvecell closed 3 months ago
2
Lack of sequences from supplementary-datadir in trees generated by phylo module

#224 AShaw1802 closed 3 months ago
2
ERROR: Failed building wheel for medaka

#223 a-qvecell closed 3 months ago
7
Large update to how initial processing paf files are parsed (implications for wt and npev calls)

#222 aineniamh opened 4 months ago
0
EPI2ME Desktop Use

#221 Ceres90 opened 4 months ago
9
Update README.md

#220 Desperate-Dan closed 4 months ago
0
Similar database sequences leading to ambiguous mappings

#219 AShaw1802 opened 4 months ago
2
Copy fq

#218 aineniamh closed 5 months ago
0
Configurable categories for grouping by, configurable header fields in detailed csv- but dynamically picks.

#217 aineniamh closed 5 months ago
0
merging main into ev_dev

#216 aineniamh closed 5 months ago
0
Copy fastq data and barcodes CSV to output folder for storage and archiving

#215 rambaut closed 5 months ago
1
fix the wpv variation plots in haplo dev so they're against cns rather than ref

#214 aineniamh closed 6 months ago
1
barcode report header bug- all same

#213 aineniamh closed 6 months ago
1
Haplo dev

#212 aineniamh closed 7 months ago
0
make category to bin by configurable- so by default ddns_group (previously display_name), but can change to species or whatever if doing EV sequencing

#211 aineniamh closed 5 months ago
2
make display_name a more sensible category: change to ddns_group

#210 aineniamh closed 7 months ago
1
smaller percentage allowable if meets read threshold

#209 aineniamh closed 7 months ago
0
min percentage not met- still make a consensus sequence

#208 aineniamh opened 7 months ago
1
if background is going to get very big with auto-accumulation, think of a way to boil it down to a smaller sample.

#207 aineniamh opened 7 months ago
0
show header fields from seqs in background and newly generated in metadata

#206 aineniamh opened 7 months ago
0
in phylo plot, strip empty fields

#205 aineniamh opened 7 months ago
0
Dont put date in supp datadir additions- just runname.fasta and runname.csv, runname may be dated

#204 aineniamh closed 7 months ago
1
runname in phylo tips

#203 aineniamh opened 7 months ago
0
position rather than genome position in snipit x axis label

#202 aineniamh closed 7 months ago
2
barcode to show in the id seqs table

#201 aineniamh closed 7 months ago
1
table only dynamically sho columns if there are any reads across samples for that ref group col

#200 aineniamh closed 7 months ago
1
new table with reads mapped/ found across all samples

#199 aineniamh closed 7 months ago
1
CoxA20 col, positive control column- so separate reference group

#198 aineniamh closed 7 months ago
2
SEQ instead of CNS for id and only show in there's mult ref group seqs per sample

#197 aineniamh closed 7 months ago
0
configure the threshold for vdpv inclusion into db

#196 aineniamh closed 7 months ago
1
Allow "notes" fields to be populated and added to the report

#195 aineniamh closed 7 months ago
1
pattern match for negative and positive- can configure this though

#194 aineniamh closed 7 months ago
1
Trivial - reduce the size of the tip dots in the phylogenetic tree

#193 rambaut closed 7 months ago
2
Control virus sequences

#192 rambaut closed 7 months ago
2
EV mode

#191 aineniamh closed 5 months ago
1
pattern match for positive or negative to flag controls

#190 aineniamh closed 7 months ago
1