Selecting between profiles
What are profiles?
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string. They are a set of "sensible defaults" for the resource requirements of each of the steps in the workflow, that can be enabled with the command line flag -profile. You can learn more about nextflow profiles at:
- https://nf-co.re/usage/configuration#basic-configuration-profiles
- https://www.nextflow.io/docs/latest/config.html#config-profiles
Available profiles
The pipeline have "standard profiles" set to run the workflows with either docker or singularity using the local executor, which is nextflow's default executor and basically runs the pipeline processes in the computer where Nextflow is launched.
If you need to run the pipeline using another executor such as sge, lsf, slurm, etc. you can take a look at nextflow's manual page to proper configure one in a new custom profile set in your personal copy of MpGAP config file and take advantage that nextflow allows multiple profiles to be used at once, e.g. -profile docker,sge.
Note
If -profile is not specified, the pipeline will run locally and expect all software to be installed and available on the PATH. This is not recommended and will most likely fail.
Note on sigularity
If you are using singularity and are persistently observing issues downloading Singularity images directly due to timeout or network issues, try downloading it first. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
This is exemplified in the installation page