issues
search
nrminor
/
oneroof
Base-, Variant-, and Consensus-calling under One Proverbial Roof. Work in progress!
MIT License
3
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Workaround for iVar not outputting separate reference segments in consensus sequences
#25
nrminor
opened
6 hours ago
0
Multi-sample coverage plotting never runs
#24
nrminor
closed
6 hours ago
1
Fix the process that checks the validity of a requested nextclade dataset
#23
nrminor
opened
6 days ago
0
Refactor so that one incomplete/unreconciled primer pair does not crash the whole run and instead allows it to proceed with what primer pairs it has
#22
nrminor
opened
6 days ago
0
Figure out how to handle malformed bed files like the BED below where all primers are forward strand oriented
#21
nrminor
opened
6 days ago
1
Add a subworkflow that bundles results for upload to SRA, Genbank, and GISAID
#20
nrminor
opened
6 days ago
0
Make sure the illumina workflow has remained up to date now that the nanopore workflow has gone through many feature adds
#19
nrminor
opened
6 days ago
0
adding a step that plots coverage across all sample
#18
akalweit5
closed
1 week ago
0
Add a Python executable entrypoint that can be used in place of Nextflow run in the pixi environment or docker container
#17
nrminor
closed
2 weeks ago
1
Enable optional email-notification-based workflow reporting
#16
nrminor
opened
3 weeks ago
0
Add reference-free branch of the pipeline that takes primer sequences alone rather than required a reference and a bed file
#15
nrminor
opened
3 weeks ago
0
Add final variant long- and pivot-table for assessing amino acid variants across samples
#14
nrminor
opened
3 weeks ago
0
Add `--help` parameter to list pipeline-specific configuration settings in the command line
#13
nrminor
closed
2 weeks ago
1
Builds fail on some systems because of cffi wheel invalid gzip header
#12
nrminor
closed
1 month ago
1
Add more exhaustive setup instructions for local and HPC execution (and eventually cloud?)
#11
nrminor
opened
2 months ago
0
Complete developer guide
#10
nrminor
opened
2 months ago
0
Output fixed y-scale and free y-scale versions of the coverage plot for multi-segment references
#9
nrminor
closed
2 months ago
0
Fix amplicon counting to enable grouping by sample when using .watchPath()
#8
nrminor
opened
3 months ago
0
Add optional vsearch deduplication
#7
nrminor
closed
1 month ago
0
Primer name normalization
#6
nrminor
opened
3 months ago
0
Primer resplicing improvements
#5
nrminor
opened
3 months ago
0
Barcode sample id lookup
#4
nrminor
opened
3 months ago
0
ARM compatibility
#3
ajlail98
opened
3 months ago
1
Coverage Plot improvements
#2
ajlail98
closed
2 months ago
0
Fixing primer resplicing
#1
ajlail98
closed
3 months ago
0