npm install
npm run serve
npm run build
npm run lint
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.
conda activate mytax2
npm run build;
docker build . -t jhuaplbio/basestack_mytax2;
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/
docker container run -it --rm -p 8098:80 jhuaplbio/basestack_mytax2 bash -c "nginx; bash "