profiles.md

Nextflow profiles

If -profile is not specified at all the pipeline will be run locally and expects all software to be installed and available in the PATH environment variable. The following -profile are available:

Define where the tools are available

conda

Build a new conda environment before running the pipeline. Use the option --condaCacheDir to change the default conda cache directory.

multiconda

Build a new conda environment for each process before running the pipeline. Use the option --condaCacheDir to change the default conda cache directory.

path

Use a global path for all tools. Use the option --globalPath to define the path the use.

multipath

Use the paths defined in configuration for each tool.

First, create a folder tree that looks like this

├── path
│   ├── alpine
│   │   └── bin
│   ├── fastqc
│   │   └── bin
│   ├── helloWorld
│   │   └── bin
│   ├── rmarkdown
│   │   └── bin
│   └── trickySoftware
│       └── bin

The second level in the folder tree is the label that has been given in each Nextflow process. Install each tool in its corresponding bin directory.

Then, use the option --globalPath to define the path to the path folder as shown above in the folder tree.

docker

Use the Docker images for each process.

singularity

Use the Singularity images for each process. Use the option --singularityImagePath to specify where the images are available.

Define where to launch the computation

By default, the pipline runs locally. If you want to run it on a computing cluster, use the profile below.

cluster

Run the workflow on the cluster, instead of locally. Use the option --queue to specify the queue where the job will be submitted.

Test the pipeline

test

Set up the test dataset.