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profiles.md

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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. The conda environment will be created in the $HOME/conda-cache-nextflow folder by default. Use the option --condaCacheDir to change the default conda cache directory.

multiconda

Build new conda environments for each process before running the pipeline. The conda environments will be created in the $HOME/conda-cache-nextflow folder by default. Use the option --condaCacheDir to change the default conda cache directory.

path

By default, Nextflow expects all the tools to be installed and available in the PATH environment variable. This path can be set using the -profile path combined with the --globalPath /my/path option specifying where the tools are installed. Assume that the pipeline has been installed in ${HOME}/tmp/myPipeline/install, geniac creates ${HOME}/tmp/myPipeline/install/path/bin folder. If you do not defined the --globalPath option, the -profile path option expect to find the tools in ${HOME}/tmp/myPipeline/install/path/bin folder.

multipath

In addition, the -profile multipath is available in order to specify the PATH for each tool, instead of a global one. Assume that the pipeline has been installed in ${HOME}/tmp/myPipeline/install, geniac creates ${HOME}/tmp/myPipeline/install/multipath folder whick look like this:

multipath/
├── alpine
│   └── bin
├── fastqc
│   └── bin
├── helloWorld
│   └── bin
├── multiqc
│   └── bin
├── python
│   └── 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.

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. Assume that the pipeline has been installed in ${HOME}/tmp/myPipeline/install, geniac creates ${HOME}/tmp/myPipeline/install/containers/singularity folder. If you ask geniac to build the singularity images, they will be stored in this folder. If you do not defined the --singularityImagePath option, the -profile singularity option expects to find the singularity images the ${HOME}/tmp/myPipeline/install/containers/singularity folder.

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.

Test the pipeline

test

Set up the test dataset