diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 3288efd..4ff3730 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,8 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh'] + steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 58a65d9..ec810d7 100644 --- a/README.md +++ b/README.md @@ -97,6 +97,7 @@ Currently documentation is available for the following systems: * [CZBIOHUB_AWS](docs/czbiohub.md) * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) * [DENBI_QBIC](docs/denbi_qbic.md) +* [GENOTOUL](docs/genotoul.md) * [GENOUEST](docs/genouest.md) * [GIS](docs/gis.md) * [HEBBE](docs/hebbe.md) diff --git a/conf/genotoul.config b/conf/genotoul.config new file mode 100644 index 0000000..75ad2c4 --- /dev/null +++ b/conf/genotoul.config @@ -0,0 +1,26 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'The Genotoul cluster profile' + config_profile_contact = 'support.bioinfo.genotoul@inra.fr' + config_profile_url = 'http://bioinfo.genotoul.fr/' +} + +singularity { + // need one image per execution + enabled = true + runOptions = '-B /bank -B /work2 -B /work -B /save -B /home' + +} + +process { + executor = 'slurm' +} + +params { + save_reference = true + igenomes_ignore = true + // Max resources requested by a normal node on genotoul. + max_memory = 120.GB + max_cpus = 48 + max_time = 96.h +} diff --git a/docs/genotoul.md b/docs/genotoul.md new file mode 100644 index 0000000..b86cf66 --- /dev/null +++ b/docs/genotoul.md @@ -0,0 +1,88 @@ +# nf-core/configs: Bioinfo Genotoul Configuration + +All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse. + +To use, run the pipeline with `-profile genotoul`. This will download and +launch the [`genotoul.config`](../conf/genotoul.config) which has been +pre-configured with a setup suitable for the Bioinfo Genotoul 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. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`. + +## Running the workflow ib the Genologin cluster + +Before running the pipeline you will need to load Nextflow and +Singularity using the environment module system on Genotoul. You can do +this by issuing the commands below: + +Once connected on our frontal node : + +```bash +# Login to a compute node +srun --mem=4G --pty bash +``` + +Setup default nextflow and singularity home directory (to be done only one time): + +```bash +sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh +``` + +Load environment : + +```bash +module purge +module load bioinfo/nfcore-Nextflow-v19.04.0 +``` + +Try a test workflow (for example the methylseq workflow) : + +```bash +nextflow run nf-core/methylseq -profile genotoul,test +``` + +Create launch script `nfcore-rnaseq.sh` : + +```bash +#!/bin/bash +#SBATCH -p workq +#SBATCH -t 1:00:00 #time in hour +#SBATCH --mem=4G +#SBATCH --mail-type=BEGIN,END,FAIL + +module load bioinfo/nfcore-Nextflow-v19.04.0 +nextflow run nf-core/methylseq -profile genotoul,test +``` + +Launch on the cluster with sbatch: + +```bash +sbatch nfcore-rnaseq.sh +``` + +## Mounted directory + +By default, available mount points are: + +* /bank +* /home +* /save +* /work +* /work2 + +To have access to specific other mount point (such as nosave or project) +you can add a config profile file with option `-profile` and which contain: + +```bash +singularity.runOptions = '-B /directory/to/mount' +``` + +## Databanks + +A local copy of several genomes are available in `/bank` directory. See +our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/) +to search for your favorite genome. + +>NB: You will need an account to use the HPC cluster on Genotoul in order +to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/). diff --git a/nfcore_custom.config b/nfcore_custom.config index 740fcc5..90145b3 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -22,8 +22,10 @@ profiles { cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } - czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; - includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" } + czbiohub_aws_highpriority { + includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; + includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"} + genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" } denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" } genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" } gis { includeConfig "${params.custom_config_base}/conf/gis.config" } @@ -48,6 +50,7 @@ params { // This is a groovy map, not a nextflow parameter set hostnames = [ crick: ['.thecrick.org'], + genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest: ['.genouest.org'], uppmax: ['.uppmax.uu.se'] ]