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conf/pipeline/eager/maestro.config
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@ -11,7 +11,6 @@ params {
config_profile_description = "Simple profiles for human nuclear or mito genomes" config_profile_description = "Simple profiles for human nuclear or mito genomes"
email = 'pluisi@pasteur.fr'
} }

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docs/maestro.md
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# nf-core/configs: Institut Pasteur Configuration on Maestro. # nf-core/configs: Maestro (at Pateur Institute, Paris) Configuration.
To use, run the pipeline with -profile maestro,<qos> (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos.
Using one of these profiles, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline
## needed Modules
Please first load java, nextflow and singularity modules
`module load java`
`module load nextflow`
`module load singularity`
Also, do not forget to run nextflow using tmux or alike.
## Other profiles at Pasteur:
If you are using TARS cluster, please refer to pasteur profile. If you are using TARS cluster, please refer to pasteur profile.
This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required
Please refer to docs/pasteur.md for installing and running nf-core instructions. Please refer to docs/pasteur.md for installing and running nf-core instructions.
Run the pipeline with -profile maestro,<qos> where qos is long or normal.

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docs/pipeline/eager/maestro.md Normal file
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# nf-core/configs: maestro eager specific configuration
Extra specific configuration for eager pipeline for human DNA data processing
## Usage
To use, run the pipeline with `-profile maestro,<qos>,<type>`, where <qos> can be normal or long and <type> can be nuclear or mitochondrial
This will download and launch the eager specific [`maestro.config`](../../../conf/pipeline/eager/maestro.config) which has been pre-configured with a setup suitable for the Maestro cluster.
Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear`
## eager specific configurations for maestro
Specific configurations for maestro has been made for eager.
We decided not to provide any Tool parameter here and focus the profile only for ressource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos so increasing the memnory and CPUs, specially for alignments).
## nuclear
Increases the number of CPUs and the amount of memory for key processes
##mitochondrial
more limited computational ressources