issues
search
BIMSBbioinfo
/
pigx_sars-cov-2
PiGx SARS-CoV-2 wastewater sequencing pipeline
GNU General Public License v3.0
18
stars
3
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Deconvolution Improvements
#115
vicfabienne
closed
2 years ago
0
clean up variant_report
#114
alexg9010
closed
1 year ago
7
sigmut_db not used anywhere, to be deleted
#113
jonasfreimuth
closed
2 years ago
2
Broken link in `CONTRIBUTING`; line 47
#112
jonasfreimuth
closed
2 years ago
4
test files in root dir
#111
jonasfreimuth
closed
2 years ago
4
packages used in `R`/`Rmd` files but not required during configure
#110
jonasfreimuth
closed
2 years ago
3
add check if databases are installed
#109
jonasfreimuth
closed
1 year ago
2
bbduk and prinseq required by `configure.ac` but not mentioned in required tools in `README.md`
#108
jonasfreimuth
closed
2 years ago
0
Add submodule step to install from source instructions in README.md
#107
jonasfreimuth
closed
2 years ago
0
Rename
#106
rekado
closed
2 years ago
0
make Filter for minimum coverage adjustable over the settings file
#105
vicfabienne
closed
1 year ago
2
VEP errors on forced rerun
#104
alexg9010
closed
1 year ago
0
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#103
thomasbtf
closed
2 years ago
1
include databases in release?
#102
alexg9010
opened
2 years ago
2
add global test
#101
alexg9010
closed
2 years ago
2
enable single end input
#100
alexg9010
closed
2 years ago
4
ivar_primer_trim rule: calculate 80% of length for trimming
#99
rcuadrat
opened
2 years ago
2
Checking for pandoc-citeproc is obsolete
#98
rekado
closed
2 years ago
2
Release tarball for 0.0.4 is incomplete
#97
rekado
closed
2 years ago
0
critical fixes
#96
vicfabienne
closed
2 years ago
0
Outputs from only *.vcf file
#95
sinclairify
opened
2 years ago
7
mutation_sheet: Write script to write a mutation sheet automatically from covidCG lists
#94
vicfabienne
opened
3 years ago
2
fix deconvolution
#93
vicfabienne
closed
2 years ago
0
Adding num of Sars-Cov-2 hits to taxonomy report
#92
mirifax
opened
3 years ago
0
fix issue#70
#91
vicfabienne
closed
2 years ago
0
enable fastq.gz input
#90
vicfabienne
closed
2 years ago
0
independent sample and read names
#89
vicfabienne
closed
2 years ago
0
add error handling if vcf file (output from lofreq) is empty, VEP should not be executed
#88
vicfabienne
closed
2 years ago
1
Enable to give sample name that is different from the read-file name
#87
vicfabienne
closed
2 years ago
0
QC reports: fix & order row/column names
#86
vicfabienne
closed
2 years ago
2
QC-report: find&fix bug that leads to negative coverage values
#85
vicfabienne
closed
2 years ago
2
documentation - variant report done
#84
vicfabienne
closed
3 years ago
0
reports: get descriptive parameters from settings-file
#83
vicfabienne
opened
3 years ago
2
needed: Stack plot giving overview over all samples despite location
#82
vicfabienne
opened
3 years ago
1
Fix stacked plot
#81
vicfabienne
closed
2 years ago
1
first part code documentation
#80
vicfabienne
closed
3 years ago
0
scoring system for quality of samples based on genome/amplicon coverage
#79
vicfabienne
closed
2 years ago
1
map plots: grey color is both for disc default and color for b6172
#78
vicfabienne
closed
3 years ago
1
stacked freq plots: values above 1
#77
vicfabienne
closed
2 years ago
2
add location labels zu discs on map plot
#76
vicfabienne
opened
3 years ago
0
rule bwa_index writes output to input directory
#75
rekado
closed
3 years ago
0
Fix Documentation link to ARTIC git repository
#74
vicfabienne
closed
3 years ago
1
Every conversion script should have at least one test
#73
rekado
closed
3 years ago
1
Fix link to the deconvolution section
#72
chaoran-chen
closed
3 years ago
1
Ressource managements
#71
vicfabienne
closed
3 years ago
1
variant_report: merge mutation frequencies when they contribute to the same aa freq
#70
vicfabienne
closed
2 years ago
3
Refine Test-sample-set
#69
vicfabienne
closed
3 years ago
1
Ideas for various convenience scripts
#68
vicfabienne
opened
3 years ago
3
Write tests and create more robust and maintainable architecture
#67
vicfabienne
opened
3 years ago
2
variant_report: Fix implementation of sigmut table deduplication
#66
vicfabienne
closed
2 years ago
4
Previous
Next