diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9ebfa5a..638e8bc 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -76,6 +76,7 @@ jobs: - 'phoenix' - 'prince' - 'rosalind' + - 'sahmri' - 'sanger' - 'seg_globe' - 'uct_hpc' diff --git a/conf/sahmri.config b/conf/sahmri.config new file mode 100644 index 0000000..b47db52 --- /dev/null +++ b/conf/sahmri.config @@ -0,0 +1,34 @@ +params { + config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.' + config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)' + config_profile_url = "https://sahmri.org.au" + max_memory = 375.GB + max_cpus = 32 + max_time = 14.d + igenomes_base = '/cancer/storage/shared/igenomes/references/' +} +process { + executor = 'slurm' + queue = 'sahmri_prod_hpc,sahmri_cancer_hpc' + maxRetries = 2 + + cpus = { check_max( 2 * task.attempt, 'cpus') } + memory = { check_max( 1.GB * task.attempt, 'memory') } + time = { check_max( 10.m * task.attempt, 'time') } +} +executor { + queueSize = 50 + submitRateLimit = '10 sec' +} +singularity { + enabled = true + autoMounts = true + beforeScript = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}' + cacheDir = '/cancer/storage/shared/simg' +} +cleanup = true +profiles { + debug { + cleanup = false + } +} diff --git a/docs/sahmri.md b/docs/sahmri.md new file mode 100644 index 0000000..4ef285e --- /dev/null +++ b/docs/sahmri.md @@ -0,0 +1,18 @@ +# nf-core/configs: SAHMRI HPC Configuration + +All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/). +To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured +with a setup suitable for the SAHMRI HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded, +and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline. + +The latest version of Nextflow is not installed by default on the SAHMRI HPC cluster. You will need to install it into a directory you have write access to. +Follow these instructions from the Nextflow documentation. + +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + +All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline +has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. + +> NB: You will need an account to use the SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk. +> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login +node. If in doubt contact ICT. diff --git a/nfcore_custom.config b/nfcore_custom.config index f154d8a..9b088b1 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -57,6 +57,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" } + sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }