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BCCDC-PHL
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ncov-tools-nf
A nextflow-based workflow for running ncov-tools
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Use pyvcf3 in cond env
#59
dfornika
closed
1 year ago
0
conda env fails to build due to pyvcf issue
#58
dfornika
closed
1 year ago
0
ncov-tools 1.9.1
#57
dfornika
closed
1 year ago
0
Update for ncov-tools v1.9
#56
dfornika
closed
1 year ago
0
Use nCoV-2019.bed
#55
dfornika
closed
2 years ago
0
Use `nCoV-2019.bed` instead of `nCoV-2019.primer.bed`
#54
dfornika
closed
2 years ago
0
Split run ID on underscores instead of fixed size
#53
dfornika
closed
2 years ago
0
`run_name` field in `summary_qc.tsv` field is appended with underscore when plate ID > 1000
#52
dfornika
closed
2 years ago
0
Add pangolearn
#51
nimbusFarzaneh
closed
3 years ago
2
Add parameter for primer scheme name
#50
dfornika
closed
3 years ago
0
Add flag for primer scheme
#49
dfornika
closed
3 years ago
0
Make pangolin update optional
#48
dfornika
closed
3 years ago
0
Make pangolin updates optional
#47
dfornika
closed
3 years ago
0
Fix CI Testing (Continued)
#46
dfornika
closed
7 months ago
0
Fix CI Testing
#45
dfornika
closed
3 years ago
1
Fix CI Testing
#44
dfornika
closed
7 months ago
1
Find negative control
#43
dfornika
closed
3 years ago
2
Negative control is not found
#42
dfornika
closed
3 years ago
1
Automatically update pangolin/pangoLEARN each time the pipeline is run
#41
dfornika
closed
3 years ago
0
Run `pangolin --update` on each pipeline run.
#40
dfornika
closed
3 years ago
0
Fix missed variants files
#39
dfornika
closed
3 years ago
0
ncov-watch summary files are not properly collected
#38
dfornika
closed
3 years ago
1
Allow user to specify that freebayes-generated consensus and variants
#37
dfornika
closed
3 years ago
0
Add freebayes-generated consensus to the 'data_root'
#36
dfornika
closed
3 years ago
0
Update to ncov-tools v1.5.1
#35
dfornika
closed
3 years ago
0
Run ncov-tools separately on each plate of samples within a sequencing run
#34
dfornika
closed
3 years ago
0
Upgrade to ncov-tools v1.5
#33
dfornika
closed
3 years ago
0
Use symlinks instead of copies in ncov-tools-input directory
#32
dfornika
closed
3 years ago
0
Add 'downsampled' mode
#31
dfornika
closed
3 years ago
0
When preparing ncov-tools-input directory, create symlinks instead of copies
#30
dfornika
closed
3 years ago
0
Bump default ncov-watchlists version
#29
dfornika
closed
3 years ago
0
Update ncov-watchlists version
#28
dfornika
closed
3 years ago
0
Update watchlist repo URL
#27
dfornika
closed
3 years ago
0
Update watchlists repo URL
#26
dfornika
closed
3 years ago
0
Replace temporary watchlists repo URL
#25
dfornika
closed
3 years ago
0
Provide mechanism to run ncov-watch on multiple watchlists and summarize the results
#24
dfornika
closed
3 years ago
0
Upgrade to ncov-tools v1.4
#23
dfornika
closed
3 years ago
0
Update to ncov-tools v.1.4
#22
dfornika
closed
3 years ago
0
Add ncov-watch script and integrate into pipeline
#21
dfornika
closed
3 years ago
1
Add 'ncov-watch.py' script to watch for variants of interest
#20
dfornika
closed
3 years ago
1
Handle case where negative control is not found
#19
dfornika
closed
3 years ago
0
Skip negative control check if no negative control sample found
#18
dfornika
closed
3 years ago
0
Two snpEff outputs not captured
#17
dfornika
closed
3 years ago
1
ncov-tools 1.3
#16
dfornika
closed
3 years ago
0
Update to ncov-tools-1.3
#15
dfornika
closed
3 years ago
0
Fix typo 2010 -> 2019
#14
dfornika
closed
3 years ago
0
Correct typo in variable name
#13
DiDigsDNA
closed
3 years ago
0
Allow completeness threshold to be set as a parameter
#12
dfornika
closed
3 years ago
0
Add parameter for primer_scheme_version
#11
dfornika
closed
3 years ago
0
Replace hard-coded ncov-tools version with a variable.
#10
DiDigsDNA
closed
3 years ago
1
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