Initiating the Core

Before starting the Core, complete all of the following:

Checklist
Access Volac's genomics server
Secure connection set up
Raw data saved in a sub-folder inside `input_core`
Sample sheet made and saved inside `input_core`

Starting the Core

First enter this command:

cd ~/genome_tools/Core

Then enter one of the following commands, depending on the file extension of your raw read data.

If the file extension of your raw read data is .fastq.gz, enter this command, replacing YYYY-MM-DD with a date:

nextflow run core.nf --indexpath 'index_YYYY-MM-DD.csv' --inputfq 'YYYY-MM-DD/*_R{1,2}_001.fastq.gz'

If the file extension of your raw read data is .fq.gz, enter this command, replacing YYYY-MM-DD with a date:

nextflow run core.nf --indexpath 'index_YYYY-MM-DD.csv' --inputfq 'YYYY-MM-DD/*_R{1,2}_001.fq.gz'

The sample sheet

Use --indexpath 'index_YYYY-MM-DD.csv' to tell the Core which sample sheet to use.

For example,

--indexpath 'index_2022-04-29.csv'

The raw data

Use --inputfq 'YYYY-MM-DD/*_R{1,2}_001.fastq.gz' to tell the Core which raw data to use.

For example,

--inputfq '2022-04-29/*_R{1,2}_001.fastq.gz'

Example

The full entry will be:

nextflow run core.nf --indexpath 'index_2022-04-29.csv' --inputfq '2022-04-29/*_R{1,2}_001.fastq.gz'

If your samples were sequenced using MiSeq technology (rather than NextSeq) an additional 5 characters are required to start the Core, _L001.

Use --inputfq 'YYYY-MM-DD/*_L001_R{1,2}_001.fastq.gz' to tell the Core which raw data to use.

Everything else remains the same.

MiSeq example

The full entry will be:

nextflow run core.nf --indexpath 'index_2022-04-29.csv' --inputfq '2022-04-29/*_L001_R{1,2}_001.fastq.gz'