From 2d102eafbc8e5b7036f614f752e507437af52d6f Mon Sep 17 00:00:00 2001 From: pierrespc Date: Fri, 8 Oct 2021 13:46:47 +0200 Subject: [PATCH] format docs --- docs/maestro.md | 9 ++++----- docs/pipeline/eager/maestro.md | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/docs/maestro.md b/docs/maestro.md index fe1b5f1..7a17064 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -1,10 +1,10 @@ -# 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, (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,` (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` @@ -12,10 +12,9 @@ Please first load java, nextflow and singularity modules 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. Please refer to docs/pasteur.md for installing and running nf-core instructions. - diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md index d272757..59af8a3 100644 --- a/docs/pipeline/eager/maestro.md +++ b/docs/pipeline/eager/maestro.md @@ -1,10 +1,10 @@ -# 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 ## Usage -To use, run the pipeline with `-profile maestro,,`, where can be normal or long and can be nuclear or mitochondrial +To use, run the pipeline with `-profile maestro,,`, 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. @@ -21,12 +21,11 @@ We decided not to provide any tool parameters here, and focus the profile only f Increases the number of CPUs and the amount of memory for key processes -##mitochondrial +## mitochondrial 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. Expect slow processes when using this profile because only 5 CPUs are available at a time. -