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Added info on dowloading pipelines

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Gwenna Breton 2022-06-30 14:24:17 +02:00 committed by GitHub
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@ -6,9 +6,43 @@ To use, run the pipeline with `-profile medair`. This will download and launch t
It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## Modules to load
## Download nf-core pipelines
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
### Set-up
First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow:
```bash
## Load Nextflow
module load nextflow/21.10.5.5658
## Load nf-core tools
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 downlonad. It will open an interactive menu. Choose `singularity` and `none` for the compression level.
### 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`
Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following:
```
export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"
```
This was also added to cronuser.
## Run nf-core pipelines
### Set-up
Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below:
```bash
## Load Nextflow and Singularity environment modules
@ -18,18 +52,13 @@ module load singularity/v3.4.0
```
>Should we link to Confluence page about new modules? See something about updating modules? etc.
>Is this a good location to mention the nf-core conda environment? module load miniconda; source activate nf-core
## 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`
Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following line: `export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"` #is that correct??
## Different profiles depending on what you are running
### Choose a 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)
## iGenomes specific configuration
>TODO modify this part. Do we want to have the iGenomes somewhere?