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connor-lab
/
ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Add variant count for each gene to qc.csv
#84
m-bull
opened
3 years ago
0
Add ability to type sequences by their variants
#83
m-bull
closed
3 years ago
0
Kubernetes process
#82
ctr26
opened
3 years ago
0
Ivar 1.3
#81
m-bull
closed
3 years ago
0
Update to ivar 1.2.4
#80
m-bull
closed
3 years ago
0
Adding mean coverage to qc.py
#79
FredDodd6
opened
3 years ago
1
Fix BAM header cleaning
#78
m-bull
closed
3 years ago
0
Switch to multistage builds for Docker and Singularity
#77
m-bull
closed
3 years ago
0
Fix up how samples are searched for using fileglobs
#76
m-bull
closed
3 years ago
0
Clean bam headers
#75
m-bull
closed
3 years ago
0
Add new option to remove samples with low reads after guppyplex
#74
m-bull
closed
3 years ago
0
Command failed: nanopolish index
#73
sthifx
closed
3 years ago
2
Oxford Nanpore data in pipeline
#72
ctr26
closed
3 years ago
2
articDownloadScheme isn't working with default URL
#71
ctr26
closed
2 years ago
7
adding -f Mark reads as QCFAIL instead of excluding them to trim.
#70
FredDodd6
opened
3 years ago
5
Nanopore tests
#69
m-bull
closed
3 years ago
0
Fix primer scheme paths after ARTIC update
#68
m-bull
closed
3 years ago
0
Error: Nextflow
#67
yockping
closed
3 years ago
1
updating ivar version to 1.2.3
#66
FredDodd6
closed
3 years ago
2
ivar 1.2.3 conda dependency conflict
#65
jts
closed
3 years ago
1
Set default illuminaKeepLen = 30
#64
m-bull
closed
3 years ago
0
Remove mpileup depth limit by default
#63
m-bull
closed
4 years ago
0
Feature/update bam to cram
#62
sb43
closed
4 years ago
0
use ivar default of 30 for illuminaKeepLen in Sanger config
#61
dkj
closed
4 years ago
1
Added libxcb, default Qt library backend for graphics rendering, to d…
#60
nodrogluap
closed
4 years ago
1
No default Qt backend for graphics when using -profile conda
#59
nodrogluap
closed
3 years ago
0
Add ampliconstats process for all the files (Samtools development branch)
#58
ac55-sanger
opened
4 years ago
1
Add minReadsPerBarcode parameter for Nanopore workflow
#57
kjsanger
closed
4 years ago
0
Qc update
#56
m-bull
closed
4 years ago
0
Update tests to compare against 5e00ba9
#55
m-bull
closed
4 years ago
0
Update ivar consensus calling mpileup command
#54
m-bull
closed
4 years ago
0
Add samtools ampliconstats feature
#53
ac55-sanger
closed
4 years ago
6
Irida/update path
#52
DarianHole
closed
4 years ago
1
Remove mpileup depth limit in consensus generation
#51
dkj
closed
4 years ago
1
Add help message and fix nanopore conda env for singularity
#50
m-bull
closed
4 years ago
0
Add initial NML Config
#49
DarianHole
closed
4 years ago
1
Remove unnecessary samtools view -bS
#48
ac55-sanger
closed
4 years ago
0
Nanopolish Pipeline keeps failing at `artic_plot_amplicon_depth` step
#47
DarianHole
closed
4 years ago
13
Compilation error on Azure (Ubuntu 18.04)
#46
delfair
closed
3 years ago
2
Feature/sb43 bam to cram
#45
sb43
closed
4 years ago
0
Allow --ref option to be a symlink.
#44
sb10
closed
4 years ago
0
add number of primer trimmed aligned reads to QC summary
#43
mgcam
closed
4 years ago
1
workflow failure w/ cmd exit status 0 and 2 (w/ cmd error exit status 125)
#42
mjpworth
closed
4 years ago
1
Fix #40: let extras.yml be found from anywhere.
#41
sb10
closed
4 years ago
2
conda profile can't find extras.yml
#40
sb10
closed
4 years ago
0
Conda env tracking
#39
m-bull
closed
4 years ago
0
Synching with fieldbioinformatics
#38
jts
closed
4 years ago
5
Use file() in Nanopore barcode detection to (hopefully) support cloud…
#37
m-bull
closed
4 years ago
0
Check for `nanoporeBarcodeDirs` doesn't work for S3 path
#36
lch14forever
opened
4 years ago
3
Add github ci test workflow, scripts and data.
#35
sb10
closed
4 years ago
1
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