Quick start commands

  1. Deposit the raw data in a sub-folder named YYYY-MM-DD/ inside input_core.
  2. Deposit the sample sheet in input_core.
  3. Set up a stable connection using tmux new -s 'name'.
  4. To run the Core:
nextflow run core.nf –-indexpath 'index_YYYY-MM-DD.csv' --inputfq 'YYYY-MM-DD/*_R{1,2}_001.fastq.gz'

Parameters

Term Description Example
--indexpath Sample sheet name 'index_2022-04-29.csv'
--inputfq Raw data location '2022-04-29/*_R{1,2}_001.fastq.gz'

Example

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

Tip

To view the Quick start instructions from the command line use:

nextflow run core.nf --help