diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b983f44..a8b6b91 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -47,13 +47,12 @@ jobs: - 'imperial_mb' - 'jax' - 'lugh' + - 'maestro' - 'mpcdf' - 'munin' - 'nu_genomics' - 'oist' - 'pasteur' - - 'pasteurNorm' - - 'pasteurLong' - 'phoenix' - 'prince' - 'sanger' diff --git a/README.md b/README.md index 2452442..e629e4a 100644 --- a/README.md +++ b/README.md @@ -116,13 +116,12 @@ Currently documentation is available for the following systems: * [ICR_DAVROS](docs/icr_davros.md) * [JAX](docs/jax.md) * [LUGH](docs/lugh.md) +* [MAESTRO](docs/maestro.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) * [NU_GENOMICS](docs/nu_genomics.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) -* [PASTEURNORM](docs/pasteurMaestroNormal.md) -* [PASTEURLONG](docs/pasteurMaestroLong.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) * [SANGER](docs/sanger.md) diff --git a/conf/maestro.config b/conf/maestro.config new file mode 100644 index 0000000..42ba030 --- /dev/null +++ b/conf/maestro.config @@ -0,0 +1,26 @@ +params { + config_profile_description = 'Institut Pasteur Maestro cluster profile' + config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA' + config_profile_contact = 'Pierre Luisi (@pierrespc)' +} + +singularity { + enabled = true + autoMounts = true + runOptions = '--home $HOME:/home/$USER --bind /pasteur' +} + +process { + executor = 'slurm' + scratch = false + queue = 'common' + clusterOptions = {task.time < 24.h ? '--qos=normal' : '--qos=long'} +} + +params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = {task.time < 24.h ? 400.GB : 100.GB } + max_cpus = {task.time < 24.h ? 96 : 5 } + max_time = {task.time < 24.h ? 24.h : 8760.h } +} diff --git a/conf/pasteurMaestroLong.config b/conf/pasteurMaestroLong.config deleted file mode 100644 index f2b8841..0000000 --- a/conf/pasteurMaestroLong.config +++ /dev/null @@ -1,26 +0,0 @@ -params { - config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_contact = 'Pierre Luisi (@pierrespc)' -} - -singularity { - enabled = true - autoMounts = true - runOptions = '--home $HOME:/home/$USER --bind /pasteur' -} - -process { - executor = 'slurm' - scratch=false - queue = "common" - clusterOptions = "--qos=long" - -} - -params { - igenomes_ignore = true - igenomesIgnore = true - max_memory = 100.GB - max_cpus = 5 - max_time = 8760.h -} diff --git a/conf/pasteurMaestroNormal.config b/conf/pasteurMaestroNormal.config deleted file mode 100644 index 049acd0..0000000 --- a/conf/pasteurMaestroNormal.config +++ /dev/null @@ -1,26 +0,0 @@ -params { - config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_contact = 'Pierre Luisi (@pierrespc)' -} - -singularity { - enabled = true - autoMounts = true - runOptions = '--home $HOME:/home/$USER --bind /pasteur' -} - -process { - executor = 'slurm' - scratch=false - queue = "common" - clusterOptions = "--qos=normal" - -} - -params { - igenomes_ignore = true - igenomesIgnore = true - max_memory = 400.GB - max_cpus = 96 - max_time = 24.h -} diff --git a/docs/maestro.md b/docs/maestro.md new file mode 100644 index 0000000..c931a05 --- /dev/null +++ b/docs/maestro.md @@ -0,0 +1,10 @@ +# nf-core/configs: Institut Pasteur Configuration on Maestro. + +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 + +I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core + +Run the pipeline with `-profile pasteur_maestro` + diff --git a/docs/pasteurMaestroLong.md b/docs/pasteurMaestroLong.md deleted file mode 100644 index 22b1bce..0000000 --- a/docs/pasteurMaestroLong.md +++ /dev/null @@ -1,8 +0,0 @@ -# nf-core/configs: Institut Pasteur Configuration on Maestro - -This is an intent for configuration of nf-core in Maestro cluster on the long qos - -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core - -Run the pipeline with `-profile pasteurLong` - diff --git a/docs/pasteurMaestroNormal.md b/docs/pasteurMaestroNormal.md deleted file mode 100644 index 91d2f45..0000000 --- a/docs/pasteurMaestroNormal.md +++ /dev/null @@ -1,8 +0,0 @@ -# nf-core/configs: Institut Pasteur Configuration on Maestro - -This is an intent for configuration of nf-core in Maestro cluster on the normal qos - -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core - -Run the pipeline with `-profile pasteurNorm` -