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polio-nanopore
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piranha
GNU General Public License v3.0
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institution configurable to show at top of report
#39
aineniamh
closed
2 years ago
0
configurable names of pos or neg control
#38
aineniamh
closed
2 years ago
1
control legend pass or not pass
#37
aineniamh
closed
2 years ago
1
select rows in the table to compile fa seqs for those samples
#36
aineniamh
closed
2 years ago
1
check the major var at a site is the one called in the cns
#35
aineniamh
closed
1 year ago
0
say what the wpv reference in the database is
#34
aineniamh
closed
1 year ago
1
only report mutations for sabin related in the first table
#33
aineniamh
closed
2 years ago
1
put the sequence in a scrollable box in the individual reports
#32
aineniamh
closed
2 years ago
0
create a homopolymer score to weight the probability of a given variant call
#31
aineniamh
closed
1 year ago
2
home alias convert to absolute path and handle spaces in path
#30
aineniamh
closed
2 years ago
1
potential alignment bug
#29
aineniamh
closed
8 months ago
2
error messages with %%
#28
aineniamh
closed
1 year ago
0
dont write to log files- just to stdout
#27
aineniamh
closed
1 year ago
0
add legend to variation plot for barcode reports
#26
aineniamh
closed
2 years ago
1
new table with calls for each sample
#25
aineniamh
closed
2 years ago
0
legend for passed or not passed controls (or icon with tick or warning symbol)
#24
aineniamh
closed
2 years ago
0
add in 'consensus' or 'vpn sequence' difference- link to respective fasta files
#23
aineniamh
closed
8 months ago
1
colour variants that are called by another colout
#22
aineniamh
closed
2 years ago
1
update snipit to id indels
#21
aineniamh
closed
1 year ago
0
use gofasta to check indels presence
#20
aineniamh
closed
1 year ago
1
poseco name by logo
#19
aineniamh
closed
2 years ago
0
hyperlink from main report to the barcode report
#18
aineniamh
closed
2 years ago
0
github action tests
#17
aineniamh
closed
2 years ago
1
make '|' a protected character on input sample/barcode
#16
aineniamh
closed
2 years ago
1
make a full list of all intermediate/ output files and rm when in overwrite mode
#15
aineniamh
closed
2 years ago
1
variant call against the new consensus sequence for haplotype calling, rather than against the reference
#14
aineniamh
closed
1 year ago
1
fasta file for each barcode into each output directory
#13
aineniamh
closed
2 years ago
1
treatment for negative control, flag if it's positive
#12
aineniamh
closed
2 years ago
0
treatment for positive control- flag if it's negative
#11
aineniamh
closed
2 years ago
0
user name on the start of the report, institution and logo potentially
#10
aineniamh
closed
2 years ago
2
cns seqs from a particular run push to the same location (publish dir)
#9
aineniamh
closed
2 years ago
1
rm read len dist
#8
aineniamh
closed
2 years ago
1
specifically flag vdpvs in the summary table, so check how many snps from sabin
#7
aineniamh
closed
2 years ago
0
landing report page- table of results, one per sample with read counts and a summary column of all positives
#6
aineniamh
closed
2 years ago
1
in haplotype pipeline, make a decision about whether haplotypes need to be called, or if it's all a single entity
#5
aineniamh
closed
1 year ago
0
consensus pipeline default (stool vs env)
#4
aineniamh
closed
2 years ago
1
print out report as pdf easily
#3
aineniamh
closed
2 years ago
1
sabin-related rather than like
#2
aineniamh
closed
2 years ago
0
Toggle cns vs haplotype pipeline
#1
aineniamh
closed
2 years ago
1
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