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Update medair.md

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- updated text about storing singularity images
- updated text about using profiles
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Gwenna Breton 2022-07-07 11:42:46 +02:00 committed by GitHub
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@ -22,23 +22,23 @@ module load miniconda
source activate nf-core 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 ### 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 ```bash
export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" 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 ## 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). 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
```