Merge pull request #321 from nf-core/combiz-patch-1

Imperial config updates

.github/workflows/main.yml

@@ -47,7 +47,6 @@ jobs:
             - 'icr_davros'
             - 'ifb_core'
             - 'imperial'
-            - 'imperial_mb'
             - 'jax'
             - 'lugh'
             - 'maestro'

README.md

@@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
 * [HASTA](docs/hasta.md)
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
+* [IMPERIAL](docs/imperial.md)
 * [JAX](docs/jax.md)
 * [LUGH](docs/lugh.md)
 * [MAESTRO](docs/maestro.md)

conf/imperial.config

@@ -7,9 +7,58 @@ params {
     config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
 
     // Resources
-  max_memory = 256.GB
+    max_memory = 480.GB
-  max_cpus = 32
+    max_cpus = 40
-  max_time = 72.h
+    max_time = 1000.h
+}
+
+profiles {
+    imperial {
+        process {
+            executor = 'pbspro'
+
+            // Process-specific resource requirements
+            withLabel:process_low {
+                // TARGET QUEUE: throughput
+                cpus   = { 2     * task.attempt }
+                memory = { 12.GB * task.attempt }
+                time   = { 4.h   * task.attempt }
+            }
+            withLabel:process_medium {
+                // TARGET QUEUE: throughput
+                cpus   = 8
+                memory = { 32.GB * task.attempt }
+                time   = { 8.h   * task.attempt }
+            }
+            withLabel:process_high {
+                // TARGET QUEUE: general
+                cpus   = 32
+                memory = { 62.GB * task.attempt }
+                time   = { 16.h  * task.attempt }
+            }
+            withLabel:process_long {
+                // TARGET QUEUE: long
+                cpus   = 8
+                memory = 96.GB
+                time   = { 72.h  * task.attempt }
+            }
+            withLabel:process_high_memory {
+                // TARGET QUEUE: large memory
+                cpus   = { 10     * task.attempt }
+                memory = { 120.GB * task.attempt }
+                time   = { 12.h   * task.attempt }
+            }
+        }
+    }
+    medbio {
+        process {
+            executor = 'pbspro'
+
+            queue = 'pqmedbio-tput'
+
+            //queue = 'med-bio' //!! this is an alias and shouldn't be used
+        }
+    }
 }
 
 executor {
@@ -20,7 +69,7 @@ executor {
     $local {
         cpus = 2
         queueSize = 1
-     memory = '32 GB'
+        memory = '6 GB'
     }
 }
 
@@ -29,9 +78,3 @@ singularity {
     autoMounts = true
     runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
 }
-
-process {
-
-  executor = 'pbspro'
-
-}

conf/imperial_mb.config

@@ -1,44 +0,0 @@
-//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

@@ -3,7 +3,7 @@
 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)'
+  config_profile_contact = 'NA'
 
   // Analysis Resource Params
   ctd_folder = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"

docs/imperial.md

@@ -2,15 +2,17 @@
 
 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.
+To use, run the pipeline with `-profile imperial,standard`. 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
+module load anaconda3/personal
+conda install -c bioconda 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.
+>NB: To submit jobs to the Imperial College MEDBIO cluster, use `-profile imperial,medbio` instead.
+>NB: You will need a restricted access account to use the HPC cluster MEDBIO.

docs/imperial_mb.md

@@ -1,16 +0,0 @@
-# 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.

nfcore_custom.config

@@ -41,7 +41,6 @@ profiles {
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
-  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }

pipeline/scflow.config

@@ -10,5 +10,4 @@
 
 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
 }