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Add IFB config

This commit is contained in:
Noirot Céline 2021-03-16 15:54:19 +01:00
parent a64dfd98c2
commit 7e9f83ee81
4 changed files with 66 additions and 1 deletions

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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow - name: Install Nextflow

24
conf/ifb_core.config Normal file
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@ -0,0 +1,24 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'The IFB core cluster profile'
config_profile_contact = 'https://community.france-bioinformatique.fr'
config_profile_url = 'https://www.france-bioinformatique.fr/'
}
singularity {
// need one image per execution
enabled = true
runOptions = '-B /shared'
}
process {
executor = 'slurm'
}
params {
igenomes_ignore = true
// Max resources requested by a normal node on genotoul.
max_memory = 240.GB
max_cpus = 28
max_time = 96.h
}

40
docs/ifb_core.md Normal file
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@ -0,0 +1,40 @@
# nf-core/configs: IFB core Configuration
All nf-core pipelines have been successfully configured for use on the IFB core at the insert institution here.
To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core cluster. 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.
## How to use on IFB core
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on IFB core. You can do this by issuing the commands below:
```bash
# Login to a compute node
srun --pty bash
## Load Nextflow and Singularity environment modules
module purge
module load nextflow/20.04.1
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
nf-core/workflow \\
-resume
-profile ifb_core \\
--email my-email@example.org \\
-c my-specific.config
...
# Or use the nf-core client
nextflow run nf-core/rnaseq ...
```
## Databanks
A local copy of several genomes are available in `/shared/bank` directory. See
our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
to search for your favorite genome.
>NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login).

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@ -24,6 +24,7 @@ profiles {
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" } ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" } icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" } genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }