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Merge pull request #146 from adrlar/master
Adding config for ICR davros cluster
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commit
adf90f3994
6 changed files with 78 additions and 1 deletions
2
.github/workflows/main.yml
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2
.github/workflows/main.yml
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
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profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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39
conf/icr_davros.config
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conf/icr_davros.config
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/*
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* -------------------------------------------------
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* Nextflow nf-core config file for ICR davros HPC
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* -------------------------------------------------
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* Defines LSF process executor and singularity
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* settings.
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*
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*/
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params {
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config_profile_description = "Nextflow nf-core profile for ICR davros HPC"
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config_profile_contact = "Adrian Larkeryd (@adrlar)"
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}
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singularity {
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enabled = true
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// runOptions = "--bind /mnt:/mnt --bind /data:/data"
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autoMounts = true
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}
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executor {
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// This is set because of an issue with too many
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// singularity containers launching at once, they
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// cause an singularity error with exit code 255.
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submitRateLimit = "2 sec"
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}
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process {
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executor = "LSF"
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}
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params {
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// LSF cluster set up with memory tied to cores,
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// it can't be requested. Locked at 12G per core.
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cpus = 10
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max_cpus = 20
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max_memory = 12.GB
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max_time = 168.h
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igenomes_base = "/mnt/scratch/readonly/igenomes"
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}
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13
conf/pipeline/sarek/icr_davros.config
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conf/pipeline/sarek/icr_davros.config
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/*
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* -------------------------------------------------
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* Nextflow nf-core config file for ICR davros HPC
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* -------------------------------------------------
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*/
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process {
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errorStrategy = {task.exitStatus in [104,134,137,139,141,143,255] ? 'retry' : 'finish'}
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maxRetries = 5
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withName:MapReads {
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memory = {check_resource(12.GB)}
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time = {check_resource(48.h * task.attempt)}
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}
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}
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docs/icr_davros.md
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docs/icr_davros.md
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@ -0,0 +1,22 @@
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# nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration
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Deployment and testing of nf-core pipelines at the Davros cluster is on-going.
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To run an nf-core pipeline on Davros, run the pipeline with `-profile icr_davros`. This will download and launch the [`icr_davros.config`](../conf/icr_davros.config) which has been pre-configured with a setup suitable for the Davros HPC 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.
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Before running the pipeline you will need to load Nextflow using the environment module system. You can do this by issuing the commands below:
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```bash
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## Load Nextflow environment modules
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module load Nextflow/19.10.0
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```
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Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity.
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A subset of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available locally on Davros so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline you want to execute. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto Davros so have a look in the `igenomes_base` path specified in [`icr_davros.config`](../conf/icr_davros.config), and if your genome of interest isn't present please contact [Scientific Computing](mailto:schelpdesk@icr.ac.uk).
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Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions).
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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 has finished successfully because it can get quite large. All of the main output files will be saved in the `results/` directory.
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>NB: Nextflow will need to submit the jobs via LSF to the HPC cluster. This can be done from an interactive or normal job. If in doubt contact Scientific Computing.
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@ -25,6 +25,7 @@ profiles {
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
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ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
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google { includeConfig "${params.custom_config_base}/conf/google.config" }
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denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
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@ -53,6 +54,7 @@ params {
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cbe: ['.cbe.vbc.ac.at'],
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cfc: ['.hpc.uni-tuebingen.de'],
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crick: ['.thecrick.org'],
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icr_davros: ['.davros.compute.estate'],
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genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
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genouest: ['.genouest.org'],
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uppmax: ['.uppmax.uu.se'],
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@ -11,4 +11,5 @@
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profiles {
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munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
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uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
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icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
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}
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