diff --git a/docs/medair.md b/docs/medair.md index 6185f64..5eb1c46 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -22,23 +22,23 @@ module load miniconda source activate nf-core ``` -### Download a pipeline - -We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` - -Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type. - ### Storage of Singularity images -When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` +When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`. -Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: +If you run or add the following to your `.bashrc`, Nexflow will know where to store the images: ```bash export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" ``` -This was also added to cronuser. +> Comment: This was also added to cronuser. + +### Download a pipeline + +We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` + +Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type. ## Run nf-core pipelines @@ -59,4 +59,8 @@ module load singularity Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). -> Usage: -profile medair,wgs ?? (Check) +For example, the following job would run with the `wgs` profile: + +```bash +run nextflow nf-core/raredisease -profile medair,wgs +```