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Add HKI profile files
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1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -62,6 +62,7 @@ jobs:
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- "google"
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- "google"
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- "hasta"
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- "hasta"
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- "hebbe"
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- "hebbe"
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- "hki"
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- "icr_davros"
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- "icr_davros"
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- "ifb_core"
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- "ifb_core"
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- "imperial"
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- "imperial"
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@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
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- [GOOGLE](docs/google.md)
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- [GOOGLE](docs/google.md)
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- [HASTA](docs/hasta.md)
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- [HASTA](docs/hasta.md)
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- [HEBBE](docs/hebbe.md)
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- [HEBBE](docs/hebbe.md)
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- [HKI](docs/hki.md)
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- [ICR_DAVROS](docs/icr_davros.md)
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- [ICR_DAVROS](docs/icr_davros.md)
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- [IMPERIAL](docs/imperial.md)
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- [IMPERIAL](docs/imperial.md)
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- [JAX](docs/jax.md)
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- [JAX](docs/jax.md)
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104
conf/hki.config
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104
conf/hki.config
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@ -0,0 +1,104 @@
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params {
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config_profile_description = 'HKI clusters profile provided by nf-core/configs.'
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_url = 'https://leibniz-hki.de'
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}
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profiles {
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apate {
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params {
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config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.'
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_url = 'https://leibniz-hki.de'
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max_memory = 128.GB
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max_cpus = 32
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max_time = 1440.h
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}
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process {
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executor = 'local'
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maxRetries = 2
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}
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executor {
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queueSize = 8
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = '/Net/Groups/ccdata/apps/singularity'
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}
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conda {
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cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
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}
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cleanup = true
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}
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aither {
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params {
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config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.'
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_url = 'https://leibniz-hki.de'
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max_memory = 128.GB
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max_cpus = 32
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max_time = 1440.h
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}
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process {
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executor = 'local'
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maxRetries = 2
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}
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executor {
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queueSize = 8
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = '/Net/Groups/ccdata/apps/singularity'
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}
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conda {
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cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
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}
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cleanup = true
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}
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arges {
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params {
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config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.'
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_url = 'https://leibniz-hki.de'
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max_memory = 64.GB
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max_cpus = 12
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max_time = 1440.h
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}
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process {
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executor = 'local'
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maxRetries = 2
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}
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executor {
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queueSize = 8
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = '/Net/Groups/ccdata/apps/singularity'
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}
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conda {
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cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
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}
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cleanup = true
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}
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debug {
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cleanup = false
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}
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}
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24
docs/hki.md
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24
docs/hki.md
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@ -0,0 +1,24 @@
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# nf-core/configs: HKI Configuration
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All nf-core pipelines have been successfully configured for use on clusters at the [Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en/).
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To use, run the pipeline with `-profile hki,<cluster>`. This will download and launch the [`hki.config`](../conf/hki.config) which contains specific profiles for each cluter. The number of parallel jobs that run is currently limited to 8.
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The profiles currently available are:
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- apate (uses singularity, cleanup set to true by default)
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- arges (uses singularity, cleanup set to true by default)
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- aither (uses singularity, cleanup set to true by default)
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- debug (sets cleanup to false for debugging purposes, use e.g. `profile hki,<cluster>,debug`)
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Note that Nextflow is not necessarily installed by default on the HKI HPC cluster(s). You will need to install it into a directory you have write access to.
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Follow these instructions from the Nextflow documentation.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
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has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
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> NB: You will need an account to use the HKI HPC clusters in order to run the pipeline. If in doubt contact the ICT Service Desk.
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> NB: Nextflow will need to submit the jobs via SLURM to the HKI HPC clusters and as such the commands above will have to be executed on the login
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> node. If in doubt contact ICT.
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@ -44,6 +44,7 @@ profiles {
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google { includeConfig "${params.custom_config_base}/conf/google.config" }
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google { includeConfig "${params.custom_config_base}/conf/google.config" }
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hasta { includeConfig "${params.custom_config_base}/conf/hasta.config" }
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hasta { includeConfig "${params.custom_config_base}/conf/hasta.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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hki { includeConfig "${params.custom_config_base}/conf/hki.config"}
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
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ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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