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Merge pull request #375 from nf-core/ifb_core-config-update

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Ifb core config update
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Sarah Guinchard 2022-05-13 14:45:44 +02:00 committed by GitHub
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2 changed files with 11 additions and 8 deletions
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11
conf/ifb_core.config
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@ -2,23 +2,22 @@
params { params {
config_profile_description = 'The IFB core cluster profile' config_profile_description = 'The IFB core cluster profile'
config_profile_contact = 'https://community.france-bioinformatique.fr' config_profile_contact = 'https://community.france-bioinformatique.fr'
config_profile_url = 'https://www.france-bioinformatique.fr/' config_profile_url = 'https://ifb-elixirfr.gitlab.io/cluster/doc/cluster-desc/'
} }
singularity { singularity {
// need one image per execution
enabled = true enabled = true
runOptions = '-B /shared' runOptions = '-B /shared'
} }
process { process {
executor = 'slurm' executor = 'slurm'
queue = { task.time <= 24.h ? 'fast' : 'long' }
} }
params { params {
igenomes_ignore = true igenomes_ignore = true
// Max resources requested by a normal node on genotoul. max_memory = 252.GB
max_memory = 240.GB max_cpus = 56
max_cpus = 28 max_time = 720.h
max_time = 96.h
} }

8
docs/ifb_core.md
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@ -6,7 +6,8 @@ To use, run the pipeline with `-profile ifb_core`. This will download and launch
## How to use on IFB core ## How to use on IFB core
Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below: Here is [the link to the cluster's documentation](https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/).
Before running the pipeline you will need to load Nextflow and other dependencies using the environment module system on IFB core. You can do this by issuing the commands below:
```bash ```bash
# Login to a compute node # Login to a compute node
@ -14,7 +15,10 @@ srun --pty bash
## Load Nextflow and Singularity environment modules ## Load Nextflow and Singularity environment modules
module purge module purge
module load nextflow/20.04.1 module load nextflow
module load singularity
module load openjdk
# Run a downloaded/git-cloned nextflow workflow from # Run a downloaded/git-cloned nextflow workflow from
nextflow run \\ nextflow run \\