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Add IFB config
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4 changed files with 66 additions and 1 deletions
2
.github/workflows/main.yml
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.github/workflows/main.yml
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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needs: test_all_profiles
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strategy:
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strategy:
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matrix:
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matrix:
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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']
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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']
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steps:
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steps:
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- uses: actions/checkout@v1
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- uses: actions/checkout@v1
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- name: Install Nextflow
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- name: Install Nextflow
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24
conf/ifb_core.config
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conf/ifb_core.config
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'The IFB core cluster profile'
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config_profile_contact = 'https://community.france-bioinformatique.fr'
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config_profile_url = 'https://www.france-bioinformatique.fr/'
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}
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singularity {
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// need one image per execution
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enabled = true
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runOptions = '-B /shared'
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}
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process {
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executor = 'slurm'
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}
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params {
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igenomes_ignore = true
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// Max resources requested by a normal node on genotoul.
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max_memory = 240.GB
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max_cpus = 28
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max_time = 96.h
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}
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40
docs/ifb_core.md
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docs/ifb_core.md
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# nf-core/configs: IFB core Configuration
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All nf-core pipelines have been successfully configured for use on the IFB core at the insert institution here.
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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.
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## How to use on IFB core
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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:
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```bash
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# Login to a compute node
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srun --pty bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load nextflow/20.04.1
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# Run a downloaded/git-cloned nextflow workflow from
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nextflow run \\
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nf-core/workflow \\
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-resume
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-profile ifb_core \\
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--email my-email@example.org \\
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-c my-specific.config
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...
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# Or use the nf-core client
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nextflow run nf-core/rnaseq ...
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```
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## Databanks
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A local copy of several genomes are available in `/shared/bank` directory. See
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our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
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to search for your favorite genome.
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>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 {
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
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ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
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imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
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genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
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genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
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