mytax2

Project setup

npm install

Compiles and hot-reloads for development

npm run serve

Compiles and minifies for production

npm run build

Lints and fixes files

npm run lint

Customize configuration

See Configuration Reference.

Samplesheet input

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. By default, it will always look in the /data/Samplesheet.csv file for your desired deployment method. For example, in dev mode it will be public/data/Samplesheet.csv, for production (like in a Docker container running nginx like what is described below) it is in <path_to_dist>/data/Samplesheet.csv. If you want to check if it is accesible, you can access it at the localhost and port with the path like localhost:8080/data/Samplesheet.csv (this is the default dev port)

The Samplesheet should look like (example below) this

sample,path_1,path_2,format,platform,database,compressed
NB11,<path_to_directory>/NB11,,directory,oxford,<path_to_database_directory>/flukraken2,
NB03,<path_to_directory>/NB03,,directory,oxford,<path_to_database_directory>/flukraken2,
ERR6913101,<path_to_directory>/ERR6913101_1.fastq.gz,<path_to_directory>/ERR6913101_2.fastq.gz,file,illumina,<path_to_database_directory>/flukraken2,
ERR6913102,<path_to_directory>/ERR6913102_1.fastq.gz,<path_to_directory>/ERR6913102_2.fastq.gz,file,illumina,<path_to_database_directory>/flukraken2,
flu_bc01,<path_to_directory>/flu_BC01.fastq,,file,oxford,<path_to_database_directory>/flukraken2,
sample,<path_to_directory>/sample_metagenome.fastq,,file,oxford,<path_to_database_directory>/flukraken2,
test,test2.fastq,,file,illumina,<path_to_database_directory>/flukraken2,

Column	Description
sample	Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (_).
path_1	Full path to FastQ file for Illumina short reads 1 OR OXFORD reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".
path_2	Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".
format	TRUE/FALSE, is the row attributed to a demultiplexed barcode folder of 1 or more fastq files or is it a single file that is .gz?
platform	Platform used, [ILLUMINA, OXFORD]
compressed	TRUE/FALSE, is your set of files compressed or not as .gz format column
pattern	Pattern to match items (regex) for barcoded runs
kits	List of guppy barcode kits for barcode runs. Such as EXP-NBD103 and SQK-LWB001

An example samplesheet has been provided with the pipeline alongside some demo data.

Creating a Docker image

conda activate mytax2

npm run build;


docker build . -t jhuaplbio/basestack_mytax2; 

Get minikraken2 database

mkdir -p data/databases
wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz -O ./data/databases/minikraken2.tar.gz 
tar -xvzf ./data/databases/minikraken2.tar.gz && rm -rf data/databases/minikraken2.tar.gz
mv minikraken2_v2_8GB_201904_UPDATE data/databases/

Running a container with the nginx service at port 8098 on localhost

docker container run -it --rm -p 8098:80 jhuaplbio/basestack_mytax2  bash -c "nginx; bash "