7  FAQ

7.1 Nextflow related

TipDo I need to activate an environment to run the pipeline?

No, the run_nextflow.sh script should automatically load the environment for you.

TipHow do I change resources (cpu, memory, time) for a workflow?

If you want to change the resources requested by a Nextflow process, update the nextflow.config in your launch directory (where you run nextflow). Configuration process selectors are used to select which processes to change resources for. The label for withName: can be the simple process name (e.g., MERYL_COUNT), the full process name (e.g., BUILD_MERYL_HIC_DATABASE:MERYL_COUNT), or a java/groovy regular expression (e.g., .*:MERYL_COUNT).

Example:

process {
  withName: `BUILD_MERYL_HIC_DATABASE:MERYL_COUNT` {
    cpus   = 50
    memory = 250.GB
    time   = 1.d
  }
}

TipHow do I change optional command-line interface (cli) parameters to tools?

Parameters for tools in Nextflow processes are either provided as process input:, or using the ext.args process directive, following the style of nf-core. Mandatory files, Optional files, and mandatory values for running a tool are supplied through process input: in which case there will be a corresponding workflow parameter to supply them if they’re user configurable. In other cases, there are optional command-line flags that could be provided. These are supplied using the process directive ext.args in the nextflow.config in your launch directory.

Example:

process {
  withName: `BUILD_MERYL_HIC_DATABASE:MERYL_COUNT` {
    ext.args = '-v'
  }
}

TipHow do I use an other branch than the main to run the pipeline?

If you want to test a pull request that was done on https://github.com/NBISweden/Earth-Biogenome-Project-pilot, you can do : Example :

BRANCH=update_report ./run_nextflow.sh