cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
PythonMIT
Pinned issues
Issues
- 1
missing "gene" keys in MPOX JSON
#177 opened by miseminger - 1
September 9, 2024 meeting notes
#180 opened by miseminger - 1
- 0
functional_annotation file fixes
#168 opened by miseminger - 0
RdRp missing for merging functional annotations
#178 opened by miseminger - 0
tidying
#179 opened by miseminger - 1
change "gene" attribute in GVF to "gene_name"
#170 opened by miseminger - 0
sample_size finding for reference mode
#166 opened by miseminger - 0
Add gene names and symbols to mutation index
#167 opened by miseminger - 0
Correct HGVS nucleotide names to be indexed from the start of the reference genome
#165 opened by miseminger - 0
addfunctions2gvf.py produces an empty file
#162 opened by miseminger - 0
- 0
Virus-MVP tasks (Madeline)
#153 opened by miseminger - 3
mutation name discrepancy
#151 opened by miseminger - 0
reevaluate adjustments to the nucleotide names
#152 opened by miseminger - 1
- 1
Update scripts to accomodate re-organized pokay
#142 opened by anwarMZ - 2
update the gff2json.py to integrate into nextflow
#141 opened by anwarMZ - 0
comb_mutation composite names
#135 opened by miseminger - 1
Missing 'ID' attribute
#132 opened by miseminger - 0
Pokay parsing
#134 opened by miseminger - 1
Add alias to the sub-lineages
#100 opened by anwarMZ - 0
- 2
Update the HGVS annotation
#102 opened by anwarMZ - 0
- 0
Collation of lineages to variants go wrong when only one lineage per variant and/or sequences from the lineage are not preset
#94 opened by anwarMZ - 0
Add recombinat lineages (XD, XE) to constellation os lineages & variants tracke and add support for surveillance reports of recombinant lineages
#95 opened by anwarMZ - 0
- 0
Pangolin module required
#81 opened by anwarMZ - 0
- 0
extract_metadata.py doesnt allow filtering data with dates for VirusSeq data portal
#76 opened by anwarMZ - 0
Add a connecting script to map sequences from VirusSeq data-portal to the lineages.
#64 opened by anwarMZ - 0
Surveillance Report
#8 opened by anwarMZ - 0
No template for bug or new feature
#63 opened by anwarMZ - 0
- 0
Error: empty files error
#47 opened by anwarMZ - 0
- 0
Limited documentation
#38 opened by anwarMZ - 2
Clade-defining info for vcf2gvf.py
#36 opened by miseminger - 0
Error in ncov_voc:vcfTogvf
#28 opened by anwarMZ - 0
- 0
Update filenames and tags in modules
#24 opened by anwarMZ - 0
Update to stable version of dsl=2
#21 opened by anwarMZ - 0
Process user-uploaded file
#16 opened by anwarMZ - 0
add single genome parsing to vcfTogvf.py
#20 opened by anwarMZ - 1
Merge Variant level files
#7 opened by anwarMZ - 1
Mutation profile for single genomes
#9 opened by anwarMZ - 0
Functional annotation using pokay
#17 opened by Anoosha-Sehar - 0
- 0
GVF to TSV file
#6 opened by anwarMZ