diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index cf00bea..41601d4 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 45721e8..5616780 100644 --- a/README.md +++ b/README.md @@ -113,6 +113,7 @@ Currently documentation is available for the following systems: * [GOOGLE](docs/google.md) * [HEBBE](docs/hebbe.md) * [ICR_DAVROS](docs/icr_davros.md) +* [JAX](docs/jax.md) * [KRAKEN](docs/kraken.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) diff --git a/conf/jax.config b/conf/jax.config new file mode 100644 index 0000000..a5437e9 --- /dev/null +++ b/conf/jax.config @@ -0,0 +1,21 @@ +params { + config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.' + config_profile_contact = 'Asaf Peer (@peera)' + config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx' + } + +executor.$slurm.queueSize = 250 +process { + executor = "slurm" + queue = "compute" + clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'} + module = "slurm" + beforeScript = 'module load singularity' +} +singularity.enabled = true +singularity.autoMounts = true +params { + max_memory = 768.GB + max_cpus = 70 + max_time = 336.h + } diff --git a/docs/jax.md b/docs/jax.md new file mode 100644 index 0000000..d38cfbe --- /dev/null +++ b/docs/jax.md @@ -0,0 +1,8 @@ +# nf-core/configs: JAX Configuration + +All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory. + +To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline and slurm will be used as well. + +>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT. +>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT. diff --git a/nfcore_custom.config b/nfcore_custom.config index a4c9939..3cafe07 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -46,6 +46,7 @@ profiles { uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } + jax { includeConfig "${params.custom_config_base}/conf/jax.config" } } // If user hostnames contain one of these substring and they are