From c0effc0366c0dce8815edc733b2143b5da1a19b6 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 14 Sep 2022 15:34:27 +0200 Subject: [PATCH] Add HKI profile files --- .github/workflows/main.yml | 1 + README.md | 1 + conf/hki.config | 104 +++++++++++++++++++++++++++++++++++++ docs/hki.md | 24 +++++++++ nfcore_custom.config | 1 + 5 files changed, 131 insertions(+) create mode 100644 conf/hki.config create mode 100644 docs/hki.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ca01a15..56755f1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -62,6 +62,7 @@ jobs: - "google" - "hasta" - "hebbe" + - "hki" - "icr_davros" - "ifb_core" - "imperial" diff --git a/README.md b/README.md index 4544b05..5264a3c 100644 --- a/README.md +++ b/README.md @@ -118,6 +118,7 @@ Currently documentation is available for the following systems: - [GOOGLE](docs/google.md) - [HASTA](docs/hasta.md) - [HEBBE](docs/hebbe.md) +- [HKI](docs/hki.md) - [ICR_DAVROS](docs/icr_davros.md) - [IMPERIAL](docs/imperial.md) - [JAX](docs/jax.md) diff --git a/conf/hki.config b/conf/hki.config new file mode 100644 index 0000000..b73558f --- /dev/null +++ b/conf/hki.config @@ -0,0 +1,104 @@ +params { + config_profile_description = 'HKI clusters profile provided by nf-core/configs.' + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_url = 'https://leibniz-hki.de' +} + +profiles { + apate { + params { + config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.' + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_url = 'https://leibniz-hki.de' + max_memory = 128.GB + max_cpus = 32 + max_time = 1440.h + } + process { + executor = 'local' + maxRetries = 2 + } + + executor { + queueSize = 8 + } + + singularity { + enabled = true + autoMounts = true + cacheDir = '/Net/Groups/ccdata/apps/singularity' + } + + conda { + cacheDir = '/Net/Groups/ccdata/apps/conda_envs' + } + + cleanup = true + } + + aither { + params { + config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.' + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_url = 'https://leibniz-hki.de' + max_memory = 128.GB + max_cpus = 32 + max_time = 1440.h + } + process { + executor = 'local' + maxRetries = 2 + } + + executor { + queueSize = 8 + } + + singularity { + enabled = true + autoMounts = true + cacheDir = '/Net/Groups/ccdata/apps/singularity' + } + + conda { + cacheDir = '/Net/Groups/ccdata/apps/conda_envs' + } + + cleanup = true + } + + arges { + params { + config_profile_description = 'apate HKI cluster profile provided by nf-core/configs.' + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_url = 'https://leibniz-hki.de' + max_memory = 64.GB + max_cpus = 12 + max_time = 1440.h + } + process { + executor = 'local' + maxRetries = 2 + } + + executor { + queueSize = 8 + } + + singularity { + enabled = true + autoMounts = true + cacheDir = '/Net/Groups/ccdata/apps/singularity' + } + + conda { + cacheDir = '/Net/Groups/ccdata/apps/conda_envs' + } + + cleanup = true + } + + debug { + cleanup = false + } +} diff --git a/docs/hki.md b/docs/hki.md new file mode 100644 index 0000000..cd102ce --- /dev/null +++ b/docs/hki.md @@ -0,0 +1,24 @@ +# nf-core/configs: HKI Configuration + +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/). + +To use, run the pipeline with `-profile hki,`. 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. + +The profiles currently available are: + +- apate (uses singularity, cleanup set to true by default) +- arges (uses singularity, cleanup set to true by default) +- aither (uses singularity, cleanup set to true by default) +- debug (sets cleanup to false for debugging purposes, use e.g. `profile hki,,debug`) + +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. +Follow these instructions from the Nextflow documentation. + +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + +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 +has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. + +> 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. +> 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 +> node. If in doubt contact ICT. diff --git a/nfcore_custom.config b/nfcore_custom.config index abf163b..d93e266 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -44,6 +44,7 @@ profiles { google { includeConfig "${params.custom_config_base}/conf/google.config" } hasta { includeConfig "${params.custom_config_base}/conf/hasta.config" } hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" } + hki { includeConfig "${params.custom_config_base}/conf/hki.config"} icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" } ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }