Merge pull request #197 from combiz/imperial

Added institutional configs for Imperial and Imperial MEDBIO.  Added …

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

conf/imperial.config

@@ -0,0 +1,37 @@
+//Profile config names for nf-core/configs
+
+params {
+  // Config Params
+  config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
+  config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
+  config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
+
+  // Resources
+  max_memory = 256.GB
+  max_cpus = 32
+  max_time = 72.h
+}
+
+executor {
+  $pbspro {
+    queueSize = 50
+  }
+
+  $local {
+     cpus = 2
+     queueSize = 1
+     memory = '32 GB'
+   }
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
+}
+
+process {
+
+  executor = 'pbspro'
+
+}

conf/imperial_mb.config

@@ -0,0 +1,44 @@
+//Profile config names for nf-core/configs
+
+params {
+  // Config Params
+  config_profile_description = 'Imperial College London - MEDBIO QUEUE - HPC Profile -- provided by nf-core/configs.'
+  config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
+  config_profile_url = 'https://www.imperial.ac.uk/bioinformatics-data-science-group/resources/uk-med-bio/'
+
+  // Resources
+  max_memory = 640.GB
+  max_cpus = 32
+  max_time = 168.h
+}
+
+executor {
+  $pbspro {
+    queueSize = 50
+  }
+
+  $local {
+    cpus = 2
+    queueSize = 1
+    memory = '32 GB'
+  }
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
+}
+
+process {
+
+  executor = 'pbspro'
+  queue = 'pqmedbio-tput'
+
+  //queue = 'med-bio' //!! this is an alias and shouldn't be used
+
+  withLabel:process_large {
+    queue = 'pqmedbio-large'
+  }
+
+}

conf/pipeline/scflow/imperial.config

@@ -0,0 +1,18 @@
+// scflow/imperial specific profile config
+
+params {
+  // Config Params
+  config_profile_description = 'Imperial College London - HPC - nf-core/scFlow Profile -- provided by nf-core/configs.'
+  config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
+
+  // Analysis Resource Params
+  ctd_folder = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"
+  ensembl_mappings = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/src/ensembl-ids/ensembl_mappings.tsv"
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/.singularity-cache"
+  runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
+}

docs/imperial.md

@@ -0,0 +1,16 @@
+# nf-core/configs: Imperial CX1 HPC Configuration
+
+All nf-core pipelines have been successfully configured for use on the CX1 cluster at Imperial College London HPC.
+
+To use, run the pipeline with `-profile imperial`. This will download and launch the [`imperial.config`](../conf/imperial.config) which has been pre-configured with a setup suitable for the CX1 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.
+
+Before running the pipeline you will need to load Nextflow using the environment module system on the CX1 cluster. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module load Nextflow
+```
+
+>NB: You will need an account to use the HPC cluster CX1 in order to run the pipeline. If in doubt contact IT.
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+>NB: To submit jobs to the Imperial College MEDBIO cluster, use `-profile imperial_mb` instead.

docs/imperial_mb.md

@@ -0,0 +1,16 @@
+# nf-core/configs: Imperial MEDBIO HPC Configuration
+
+All nf-core pipelines have been successfully configured for use on the MEDBIO cluster at Imperial College London HPC.
+
+To use, run the pipeline with `-profile imperial_mb`. This will download and launch the [`imperial_mb.config`](../conf/imperial_mb.config) which has been pre-configured with a setup suitable for the MEDBIO 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.
+
+Before running the pipeline you will need to load Nextflow using the environment module system on the head node. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module load Nextflow
+```
+
+>NB: You will need an account to use the HPC cluster MEDBIO in order to run the pipeline. Access to the MEDBIO queue is exclusive.  If in doubt contact IT.
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+>NB: To submit jobs to the standard CX1 cluster at Imperial College, use `-profile imperial` instead.

docs/pipeline/scflow/imperial.md

@@ -0,0 +1,21 @@
+# nf-core/configs: Imperial scflow Specific Configuration
+
+Extra specific configuration for the scflow pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile imperial` or `-profile imperial_mb`.
+
+This will download and launch the scflow specific [`imperial.config`](../../../conf/pipeline/scflow/imperial.config) which has been pre-configured with a setup suitable for the Imperial HPC cluster.
+
+Example: `nextflow run nf-core/scflow -profile imperial`
+
+## scflow specific configurations for Imperial
+
+Specific configurations for Imperial have been made for scflow.
+
+* Singularity `enabled` and `autoMounts` set to `true`
+* Singularity `cacheDir` path set to an RDS location
+* Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
+* Params `ctd_folder` set to an RDS location.
+* Parms `ensembl_mappings` set to an RDS location.

nfcore_custom.config

@@ -24,6 +24,8 @@ profiles {
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
+  imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
+  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
@@ -54,6 +56,8 @@ params {
     cfc: ['.hpc.uni-tuebingen.de'],
     crick: ['.thecrick.org'],
     icr_davros: ['.davros.compute.estate'],
+    imperial: ['.hpc.ic.ac.uk'],
+    imperial_mb: ['.hpc.ic.ac.uk'],
     genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],
     uppmax: ['.uppmax.uu.se'],

pipeline/scflow.config

@@ -0,0 +1,14 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/scflow custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/scflow folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  imperial { includeConfig "${params.custom_config_base}/conf/pipeline/scflow/imperial.config" }
+  imperial_mb { includeConfig "${params.custom_config_base}/conf/pipeline/scflow/imperial.config" } // intended
+}