connor-lab ncov2019-artic-nf issues

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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issues

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Executions fails because Nextflow preview function is deprecated

#134 alethomas opened 4 months ago
0
Nanopore update

#133 JD2112 closed 8 months ago
0
Update config

#132 sofstam closed 9 months ago
0
Update Syntax for Compatibility with Nextflow 23.04.4

#131 eptroendle opened 9 months ago
0
Update nextclade 2.11

#130 sofstam closed 1 year ago
0
Add nextflow dependency

#129 pdp10 opened 1 year ago
0
Fix dsl2 syntax errors

#128 rdeborja opened 1 year ago
1
Sc2reporter comp

#127 LordRust closed 1 year ago
1
Enable medaka to run V4 primer scheme

#126 pdp10 opened 1 year ago
0
Enable medaka to run V4 primer scheme

#125 pdp10 closed 1 year ago
0
Run versions process with nanopore medaka

#124 henningonsbring closed 1 year ago
1
Update pangolin container

#123 sofstam closed 1 year ago
0
Downgrade nextclade

#122 henningonsbring closed 2 years ago
1
Fixing git aln2typeversion

#121 JezSw closed 2 years ago
0
Update dockerfile

#120 sofstam closed 2 years ago
0
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

#119 thomasbtf opened 2 years ago
0
fix: update to artic 1.2.2

#118 thomasbtf opened 2 years ago
0
A new release for this pipeline ?

#117 valentinelsra opened 2 years ago
2
Pin pip version in environment.yml

#116 MattBashton opened 2 years ago
0
Completeness field to report JSON

#115 bede closed 2 years ago
1
Adding nCoV-2019.primer.bed for analysis with midnight primer scheme

#114 henningonsbring closed 2 years ago
1
uploaded dag

#113 JD2112 closed 2 years ago
0
Added channel_priority help

#112 BioWilko closed 2 years ago
0
readgroup not found in provided primer scheme (1) for V4 scheme

#111 esha-joshi opened 2 years ago
5
GFF included repo doesn't include ORF1ab frameshift

#110 tnguyensanger opened 3 years ago
0
Add github action to build a Docker image and update for Nextflow 21.04.1

#109 antunderwood opened 3 years ago
0
Guppyplex step not working

#108 KevinMenden closed 3 years ago
0
nextclade added to the pipeline

#107 JD2112 closed 3 years ago
0
Medaka sp3

#106 nick297 closed 3 years ago
0
New protocolo Nanopore V1200

#105 ghost opened 3 years ago
0
Unparseable date error

#104 wtmatlock opened 3 years ago
1
variants with low SupportFraction change the sequence

#103 paraslonic opened 3 years ago
0
Snakemake file

#102 ksw9 opened 3 years ago
1
Variant definitions

#101 m-bull opened 3 years ago
0
Illumina

#100 dianalir opened 3 years ago
0
Fix params.gff undefined and remove CLIMB upload

#99 m-bull closed 3 years ago
0
Accidental pull request. Ignore me.

#98 sylvinite closed 3 years ago
0
Nanopore-conda-environment.yaml update

#97 tarah28 opened 3 years ago
0
Failed samples

#96 gdauria opened 3 years ago
0
docker profile not working

#95 rrdavis77 opened 3 years ago
3
Access to undefined parameter 'gff'

#94 hodeco opened 3 years ago
2
Using the pipeline for non-artic primers?!

#93 ahmedmagds closed 3 years ago
2
Frameshift variants may interfere with typing in type_vcf.py, even with low ALT_FREQ

#92 dfornika opened 3 years ago
7
Handle variants with consequence type 'stop_retained' as synonymous variants.

#91 dfornika closed 3 years ago
0
type_vcf.py doesn't handle variants with consequence 'stop_retained'

#90 dfornika closed 3 years ago
0
Make QC cutoffs configurable, but with sensible defaults

#89 m-bull opened 3 years ago
0
Add --force-no-qc flag

#88 m-bull opened 3 years ago
0
Sample names inherit part of illumina's nomenclature for index and lane

#87 MattBashton opened 3 years ago
0
Error: prepareReferenceFiles

#86 yockping opened 3 years ago
4
Update documentation

#85 m-bull opened 3 years ago
0