diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index aa11e4e..ac31dfe 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -66,6 +66,7 @@ jobs: - "jax" - "lugh" - "marvin" + - "mjolnir_globe" - "maestro" - "mpcdf" - "munin" diff --git a/README.md b/README.md index c42981e..1f37d29 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,7 @@ Currently documentation is available for the following systems: - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [MARVIN](docs/marvin.md) +- [MJOLNIR_GLOBE](docs/mjolnir_globe.md) - [MPCDF](docs/mpcdf.md) - [MUNIN](docs/munin.md) - [NU_GENOMICS](docs/nu_genomics.md) diff --git a/conf/mjolnir_globe.config b/conf/mjolnir_globe.config new file mode 100644 index 0000000..0f30313 --- /dev/null +++ b/conf/mjolnir_globe.config @@ -0,0 +1,25 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Section for Hologenomics and Section for Molecular Ecology and Evolution @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.' + config_profile_contact = 'Aashild Vaagene (@ashildv)' + config_profile_url = 'https://globe.ku.dk/research/' + max_memory = 500.GB + max_cpus = 50 + max_time = 720.h +} + +singularity { + enabled = true + autoMounts = true + cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity' +} + +process { + executor = 'slurm' +} + +cleanup = true + +executor { + queueSize = 10 +} diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md new file mode 100644 index 0000000..487819a --- /dev/null +++ b/docs/mjolnir_globe.md @@ -0,0 +1,31 @@ +# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration + +> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT. + +Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below). + +The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space. +If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files. + +The following lines **must** be added by users to their `~/.bash_profile`: + +```bash +#re-direct tmp files away from /tmp directories on compute nodes or the headnode +export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore + +# nextflow - limiting memory of virtual java machine +NXF_OPTS='-Xms1g -Xmx4g' +``` + +Once you have created the `.tmp_nfcore` directory and added the above lines of code to your `.bash_profile` you can run an nf-core pipeline. + +Before running a pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: + +```bash +## Load Java and Nextflow environment modules +module purge +module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556 +``` + +All of the intermediate output files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. +The `mjolnir_globe` config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. diff --git a/nfcore_custom.config b/nfcore_custom.config index a659638..88e7227 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -49,6 +49,7 @@ profiles { lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } + mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } nihbiowulf { includeConfig "${params.custom_config_base}/conf/nihbiowulf.config" }