https://github.com/connor-lab/ncov2019-artic-nf
Revision 9f3f9fac98f4307d56f63c587b64116d69b094b2 authored by Matt Bull on 19 March 2020, 19:16:17 UTC, committed by Matt Bull on 19 March 2020, 19:16:17 UTC
1 parent 50f561d
Tip revision: 9f3f9fac98f4307d56f63c587b64116d69b094b2 authored by Matt Bull on 19 March 2020, 19:16:17 UTC
Add an illumina bam/consensus workflow using iVar
Add an illumina bam/consensus workflow using iVar
Tip revision: 9f3f9fa
environment.yml
name: artic-ncov2019
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python=3
- nodejs=12
- biopython=1.74
- bwa=0.7.17=pl5.22.0_2
- clint=0.5.1=py36_0
- eigen=3.2=3
- pysam=0.15.3
- pyvcf=0.6.8=py36_0
- ete3=3.1.1=py36_0
- goalign=0.2.8=0
- gotree=0.2.10=0
- libdeflate=1.3
- muscle=3.8.1551=2
- nanopolish=0.11.3
- phyml=3.3.20190909 # references etetoolkit build
- pandas=0.23.0=py36_1
- samtools=1.9
- mafft=7.407=0
- iqtree=1.6.12
- datrie=0.8
- snakemake-minimal=5.8.1
- minimap2=2.17
- artic-network::rampart=1.0
- pip
- pip:
- git+https://github.com/artic-network/fieldbioinformatics.git
- git+https://github.com/artic-network/Porechop.git@v0.3.2pre
- binlorry==1.3.0_alpha1
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