diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config index 473eec3..3705d8c 100644 --- a/conf/pipeline/eager/maestro.config +++ b/conf/pipeline/eager/maestro.config @@ -11,7 +11,6 @@ params { config_profile_description = "Simple profiles for human nuclear or mito genomes" - email = 'pluisi@pasteur.fr' } diff --git a/docs/maestro.md b/docs/maestro.md index 59daa80..fe1b5f1 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -1,10 +1,21 @@ -# 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, (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. -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. -Run the pipeline with -profile maestro, where qos is long or normal. diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md new file mode 100644 index 0000000..45a151e --- /dev/null +++ b/docs/pipeline/eager/maestro.md @@ -0,0 +1,29 @@ +# 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,,`, where can be normal or long and 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 + +