From 453080f28210b38e4b0465d4bb3fb387a1489e3a Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 3 Feb 2022 18:26:30 +0000
Subject: [PATCH 01/16] Update imperial.config

Removed my contact details.  Users can request help on the nf-core slack.
---
 conf/imperial.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index eeb98ae..312544a 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -3,7 +3,7 @@
 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_contact = 'NA'
   config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
 
   // Resources

From 731f86e7f1a9bbad9fe968fd613876a5580eaccd Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 3 Feb 2022 18:27:49 +0000
Subject: [PATCH 02/16] Update imperial_mb.config

Removed my contact details.  Users can request help on the nf-core slack.
---
 conf/imperial_mb.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/imperial_mb.config b/conf/imperial_mb.config
index a89ffcd..afd88c1 100644
--- a/conf/imperial_mb.config
+++ b/conf/imperial_mb.config
@@ -3,7 +3,7 @@
 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_contact = 'NA'
   config_profile_url = 'https://www.imperial.ac.uk/bioinformatics-data-science-group/resources/uk-med-bio/'
 
   // Resources

From 2bdf5863d93a849abd39859fac36e4f36f904c1f Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 3 Feb 2022 18:28:11 +0000
Subject: [PATCH 03/16] Update imperial.config

Removed my contact details.  Users can request help on the nf-core slack.
---
 conf/pipeline/scflow/imperial.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/pipeline/scflow/imperial.config b/conf/pipeline/scflow/imperial.config
index 7f46466..78a4a8b 100644
--- a/conf/pipeline/scflow/imperial.config
+++ b/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/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"
@@ -15,4 +15,4 @@ singularity {
   autoMounts = true
   cacheDir = "/rds/general/user/$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"
-}
\ No newline at end of file
+}

From 81a273c730505b421ca05e0485eca7282d18d5e6 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 3 Feb 2022 18:31:02 +0000
Subject: [PATCH 04/16] Update imperial_mb.config

Dropped support for pqmedbio-large which is not currently available.
---
 conf/imperial_mb.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/imperial_mb.config b/conf/imperial_mb.config
index afd88c1..72bc412 100644
--- a/conf/imperial_mb.config
+++ b/conf/imperial_mb.config
@@ -37,8 +37,8 @@ process {
 
   //queue = 'med-bio' //!! this is an alias and shouldn't be used
 
-  withLabel:process_large {
-    queue = 'pqmedbio-large'
-  }
+  //withLabel:process_large {
+    //queue = 'pqmedbio-large' //!! this queue is unavailable as of Feb 2022
+  //}
 
 }

From fe5474a029c63b7bf22426fe56b570a615fd81dd Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 10 Feb 2022 23:02:47 +0000
Subject: [PATCH 05/16] Update imperial.config

Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
---
 conf/imperial.config | 71 +++++++++++++++++++++++++++++++-------------
 1 file changed, 50 insertions(+), 21 deletions(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index 312544a..e2a3aca 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -1,37 +1,66 @@
 //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 = 'NA'
-  config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
+    // Config Params
+    config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
+    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
+    // Resources
+    max_memory = 480.GB
+    max_cpus = 40
+    max_time = 1000.h
 }
 
 executor {
-  $pbspro {
-    queueSize = 50
-  }
+    $pbspro {
+        queueSize = 50
+    }
 
-  $local {
-     cpus = 2
-     queueSize = 1
-     memory = '32 GB'
-   }
+    $local {
+        cpus = 2
+        queueSize = 1
+        memory = '6 GB'
+    }
 }
 
 singularity {
-  enabled = true
-  autoMounts = true
-  runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
+    enabled = true
+    autoMounts = true
+    runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
 }
 
 process {
+    executor = 'pbspro'
 
-  executor = 'pbspro'
-
+    // Process-specific resource requirements
+    withLabel:process_low {
+        // TARGET QUEUE: throughput
+        cpus   = { check_max( 2     * task.attempt,  'cpus'   ) }
+        memory = { check_max( 12.GB * task.attempt,  'memory' ) }
+        time   = { check_max( 4.h   * task.attempt,  'time'   ) }
+    }
+    withLabel:process_medium {
+        // TARGET QUEUE: throughput
+        cpus   = { check_max( 8,                     'cpus'   ) }
+        memory = { check_max( 32.GB * task.attempt,  'memory' ) }
+        time   = { check_max( 8.h   * task.attempt,  'time'   ) }
+    }
+    withLabel:process_high {
+        // TARGET QUEUE: general
+        cpus   = { check_max( 32,                    'cpus'   ) }
+        memory = { check_max( 62.GB * task.attempt,  'memory' ) }
+        time   = { check_max( 16.h  * task.attempt,  'time'   ) }
+    }
+    withLabel:process_long {
+        // TARGET QUEUE: long
+        cpus   = { check_max( 8,                     'cpus'   ) }
+        memory = { check_max( 96.GB,                 'memory' ) }
+        time   = { check_max( 72.h  * task.attempt,  'time'   ) }
+    }
+    withLabel:process_high_memory {
+        // TARGET QUEUE: large memory
+        cpus   = { check_max( 10     * task.attempt, 'cpus'   ) }
+        memory = { check_max( 120.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 12.h   * task.attempt, 'time'   ) }
+    }
 }

From e1d0bf0cd2b4156a6dd8922630bdb8521744a973 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 10 Feb 2022 23:44:49 +0000
Subject: [PATCH 06/16] Delete imperial_mb.config

Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
---
 conf/imperial_mb.config | 44 -----------------------------------------
 1 file changed, 44 deletions(-)
 delete mode 100644 conf/imperial_mb.config

diff --git a/conf/imperial_mb.config b/conf/imperial_mb.config
deleted file mode 100644
index 72bc412..0000000
--- a/conf/imperial_mb.config
+++ /dev/null
@@ -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 = 'NA'
-  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' //!! this queue is unavailable as of Feb 2022
-  //}
-
-}

From 38a05a6531051067a4c97e2fa8561899cfdf61fd Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 10 Feb 2022 23:46:14 +0000
Subject: [PATCH 07/16] Update imperial.config

Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
---
 conf/imperial.config | 114 ++++++++++++++++++++++++++-----------------
 1 file changed, 70 insertions(+), 44 deletions(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index e2a3aca..26742f2 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -1,14 +1,76 @@
 //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_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
+profiles {
+    imperial {
+        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 = 480.GB
-    max_cpus = 40
-    max_time = 1000.h
+            // Resources
+            max_memory = 480.GB
+            max_cpus = 40
+            max_time = 1000.h
+        }
+
+        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 {
+        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 = 480.GB
+            max_cpus = 40
+            max_time = 1000.h
+        }
+
+        process {
+            executor = 'pbspro'
+
+            queue = 'pqmedbio-tput'
+
+        //queue = 'med-bio' //!! this is an alias and shouldn't be used
+        }
+    }
 }
 
 executor {
@@ -28,39 +90,3 @@ singularity {
     autoMounts = true
     runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
 }
-
-process {
-    executor = 'pbspro'
-
-    // Process-specific resource requirements
-    withLabel:process_low {
-        // TARGET QUEUE: throughput
-        cpus   = { check_max( 2     * task.attempt,  'cpus'   ) }
-        memory = { check_max( 12.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 4.h   * task.attempt,  'time'   ) }
-    }
-    withLabel:process_medium {
-        // TARGET QUEUE: throughput
-        cpus   = { check_max( 8,                     'cpus'   ) }
-        memory = { check_max( 32.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 8.h   * task.attempt,  'time'   ) }
-    }
-    withLabel:process_high {
-        // TARGET QUEUE: general
-        cpus   = { check_max( 32,                    'cpus'   ) }
-        memory = { check_max( 62.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 16.h  * task.attempt,  'time'   ) }
-    }
-    withLabel:process_long {
-        // TARGET QUEUE: long
-        cpus   = { check_max( 8,                     'cpus'   ) }
-        memory = { check_max( 96.GB,                 'memory' ) }
-        time   = { check_max( 72.h  * task.attempt,  'time'   ) }
-    }
-    withLabel:process_high_memory {
-        // TARGET QUEUE: large memory
-        cpus   = { check_max( 10     * task.attempt, 'cpus'   ) }
-        memory = { check_max( 120.GB * task.attempt, 'memory' ) }
-        time   = { check_max( 12.h   * task.attempt, 'time'   ) }
-    }
-}

From 14c7662762601298ecd9fc18dbd173212c742be8 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 10 Feb 2022 23:49:43 +0000
Subject: [PATCH 08/16] Update imperial.md

Updated docs to reflect restructuring for internal profiles
---
 docs/imperial.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/imperial.md b/docs/imperial.md
index 43fc117..fe7883a 100644
--- a/docs/imperial.md
+++ b/docs/imperial.md
@@ -8,9 +8,11 @@ Before running the pipeline you will need to load Nextflow using the environment
 
 ```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: You will need a restricted access account to use the HPC cluster MEDBIO.

From 5aa1abda26f4d14598bc47b587d4a010c9719a13 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 00:07:05 +0000
Subject: [PATCH 09/16] Delete imperial_mb.md

Deprecated in favour of internal profiles within the single imperial.config
---
 docs/imperial_mb.md | 16 ----------------
 1 file changed, 16 deletions(-)
 delete mode 100644 docs/imperial_mb.md

diff --git a/docs/imperial_mb.md b/docs/imperial_mb.md
deleted file mode 100644
index d7f7f15..0000000
--- a/docs/imperial_mb.md
+++ /dev/null
@@ -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.

From 34d9e7a967132e5006362c938ad8d3a609bc5fc6 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 00:08:08 +0000
Subject: [PATCH 10/16] Update imperial.md

Updated docs to reflect use of internal profiles
---
 docs/imperial.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/imperial.md b/docs/imperial.md
index fe7883a..158827c 100644
--- a/docs/imperial.md
+++ b/docs/imperial.md
@@ -2,7 +2,7 @@
 
 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:
 
@@ -14,5 +14,5 @@ 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.

From c5e4ac2025a633e7ba2820d4381a0e7a65dc5852 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 00:25:44 +0000
Subject: [PATCH 11/16] Update scflow.config

Removed line corresponding to profile deprecated by change to internal profiles
---
 pipeline/scflow.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pipeline/scflow.config b/pipeline/scflow.config
index 8c4697f..0ff19ea 100644
--- a/pipeline/scflow.config
+++ b/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
-}
\ No newline at end of file
+}

From b99b74b2d38045f4737e24f385c4f141ce4a0c24 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 00:26:45 +0000
Subject: [PATCH 12/16] Update imperial.config

Fixed indent
---
 conf/imperial.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index 26742f2..9f560e0 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -68,7 +68,7 @@ profiles {
 
             queue = 'pqmedbio-tput'
 
-        //queue = 'med-bio' //!! this is an alias and shouldn't be used
+            //queue = 'med-bio' //!! this is an alias and shouldn't be used
         }
     }
 }

From f33bc965d65fc2527da7dd7510add7072118292b Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 09:32:50 +0000
Subject: [PATCH 13/16] Update nfcore_custom.config

Removed deprecated medbio config
---
 nfcore_custom.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nfcore_custom.config b/nfcore_custom.config
index f580206..a242948 100644
--- a/nfcore_custom.config
+++ b/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" }

From 8937699abe617297743272e5baf2f90bd86b45d3 Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 09:33:54 +0000
Subject: [PATCH 14/16] Update README.md

Added imperial docs link
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index f2accc6..d0e703f 100644
--- a/README.md
+++ b/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)

From 683564de1baac42ffc789232e0944d9edd80055b Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 09:35:18 +0000
Subject: [PATCH 15/16] Update main.yml

Removed deprecated imperial medbio from GHA
---
 .github/workflows/main.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a3b41fd..9f260cd 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -47,7 +47,6 @@ jobs:
             - 'icr_davros'
             - 'ifb_core'
             - 'imperial'
-            - 'imperial_mb'
             - 'jax'
             - 'lugh'
             - 'maestro'

From 3ce32f50c45b44ca1226f1a60b6cf821a26315df Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Fri, 11 Feb 2022 11:02:40 +0000
Subject: [PATCH 16/16] Update imperial.config

Moved params configs from internal profile to universal
---
 conf/imperial.config | 36 ++++++++++++------------------------
 1 file changed, 12 insertions(+), 24 deletions(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index 9f560e0..729d623 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -1,19 +1,19 @@
 //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 = 480.GB
+    max_cpus = 40
+    max_time = 1000.h
+}
+
 profiles {
     imperial {
-        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 = 480.GB
-            max_cpus = 40
-            max_time = 1000.h
-        }
-
         process {
             executor = 'pbspro'
 
@@ -51,18 +51,6 @@ profiles {
         }
     }
     medbio {
-        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 = 480.GB
-            max_cpus = 40
-            max_time = 1000.h
-        }
-
         process {
             executor = 'pbspro'