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docs/maestro.md
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# nf-core/configs: Maestro (at Pateur Institute, Paris) Configuration. # 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. 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 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 ## needed Modules
Please first load java, nextflow and singularity modules Please first load java, nextflow and singularity modules
`module load java` `module load java`
`module load nextflow` `module load nextflow`
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Also, do not forget to run nextflow using tmux or alike. Also, do not forget to run nextflow using tmux or alike.
## Other profiles at Pasteur
## 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.
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.

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docs/pipeline/eager/maestro.md
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# nf-core/configs: maestro eager specific configuration # nf-core/configs maestro eager specific configuration
Extra specific configuration for eager pipeline for human DNA data processing Extra specific configuration for eager pipeline for human DNA data processing
## Usage ## 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 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. 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.
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Increases the number of CPUs and the amount of memory for key processes Increases the number of CPUs and the amount of memory for key processes
##mitochondrial ## mitochondrial
More limited computational resources More limited computational resources
##unlimitedtime ## unlimitedtime
Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles. Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles.
Expect slow processes when using this profile because only 5 CPUs are available at a time. Expect slow processes when using this profile because only 5 CPUs are available at a time.