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https://github.com/MillironX/nf-configs.git
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commit
9b2d5bfead
5 changed files with 32 additions and 1 deletions
2
.github/workflows/main.yml
vendored
2
.github/workflows/main.yml
vendored
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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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']
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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']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
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* [GOOGLE](docs/google.md)
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* [HEBBE](docs/hebbe.md)
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* [ICR_DAVROS](docs/icr_davros.md)
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* [JAX](docs/jax.md)
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* [KRAKEN](docs/kraken.md)
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* [MPCDF](docs/mpcdf.md)
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* [MUNIN](docs/munin.md)
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21
conf/jax.config
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21
conf/jax.config
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@ -0,0 +1,21 @@
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params {
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config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
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config_profile_contact = 'Asaf Peer (@peera)'
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config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
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}
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executor.$slurm.queueSize = 250
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process {
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executor = "slurm"
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queue = "compute"
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clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
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module = "slurm"
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beforeScript = 'module load singularity'
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}
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singularity.enabled = true
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singularity.autoMounts = true
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params {
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max_memory = 768.GB
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max_cpus = 70
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max_time = 336.h
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}
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8
docs/jax.md
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8
docs/jax.md
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@ -0,0 +1,8 @@
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# nf-core/configs: JAX Configuration
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All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
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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.
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>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
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>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.
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@ -46,6 +46,7 @@ profiles {
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uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
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utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
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uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
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jax { includeConfig "${params.custom_config_base}/conf/jax.config" }
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}
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// If user hostnames contain one of these substring and they are
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