From 9d46ee97fc34ceb7743ee2c27af11f2175bf2e0d Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 26 Sep 2025 11:49:08 +0000
Subject: [PATCH 01/17] Newcastle_dry_run

---
 .github/workflows/main.yml |  1 +
 conf/newcastle.config      | 20 ++++++++++++++++++++
 docs/newcastle.md          | 20 ++++++++++++++++++++
 nfcore_custom.config       |  3 +++
 4 files changed, 44 insertions(+)
 create mode 100644 conf/newcastle.config
 create mode 100644 docs/newcastle.md

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 09ccec31f..a6348d609 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -128,6 +128,7 @@ jobs:
           - "mssm"
           - "munin"
           - "nci_gadi"
+          - "newcastle"
           - "nu_genomics"
           - "nygc"
           - "nyu_hpc"
diff --git a/conf/newcastle.config b/conf/newcastle.config
new file mode 100644
index 000000000..4fe5dcb97
--- /dev/null
+++ b/conf/newcastle.config
@@ -0,0 +1,20 @@
+params {
+    config_profile_description = 'Crop Diversity HPC cluster profile'
+    config_profile_contact = 'Thomas Adams (@TMAdams), Moray Smith (@SwiftSeal), Miriam Schreiber (@SchreiberM)'
+    config_profile_url = 'https://help.cropdiversity.ac.uk/'
+}
+
+executor {
+    name = 'slurm'
+}
+
+process {
+    scratch = true
+    errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
+}
+
+singularity {
+    enabled = true
+    pullTimeout = '2 h'
+    autoMounts = true
+}
diff --git a/docs/newcastle.md b/docs/newcastle.md
new file mode 100644
index 000000000..07a9ca492
--- /dev/null
+++ b/docs/newcastle.md
@@ -0,0 +1,20 @@
+# nf-core/configs: Newcastle HPC Configuration
+
+Configuration for the Newcastle high performance computing (HPC) cluster.
+
+## Setup
+
+Prior to using nextflow, please follow the instructions on the installing conda.
+< to be completed >
+
+We advise either creating a conda environment containing nextflow, or installing nextflow in your base environment if this is not possible.
+
+## Run
+
+To use this profile, simply pass Nextflow the -profile newcastle flag eg.
+
+```bash
+nextflow run nf-core/_pipeline_ -profile newcastle --outdir results
+```
+
+In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) on ecoflow.ucl@gmail.com . We are at UCL, but helped set this up.
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 229b06fa2..d7fdcb729 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -292,6 +292,9 @@ profiles {
     nci_gadi {
         includeConfig "${params.custom_config_base}/conf/nci_gadi.config"
     }
+    newcastle {
+        includeConfig "${params.custom_config_base}/conf/newcastle.config"
+    }
     nu_genomics {
         includeConfig "${params.custom_config_base}/conf/nu_genomics.config"
     }

From bafb6979a9e585a8a035929265319d5eee644227 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 26 Sep 2025 15:04:54 +0200
Subject: [PATCH 02/17] Update newcastle.config

---
 conf/newcastle.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index 4fe5dcb97..b196edf2e 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,7 +1,7 @@
 params {
-    config_profile_description = 'Crop Diversity HPC cluster profile'
-    config_profile_contact = 'Thomas Adams (@TMAdams), Moray Smith (@SwiftSeal), Miriam Schreiber (@SchreiberM)'
-    config_profile_url = 'https://help.cropdiversity.ac.uk/'
+    config_profile_description = 'Newcastle HPC cluster profile'
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)'
+    config_profile_url = ''
 }
 
 executor {

From 880753dcd3ba8b0533cb404574a38f01cd4e7b2d Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 26 Sep 2025 15:15:50 +0200
Subject: [PATCH 03/17] Update newcastle.config

---
 conf/newcastle.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index b196edf2e..17ec1e842 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -11,6 +11,8 @@ executor {
 process {
     scratch = true
     errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
+    queue   = 'defq'                    // maps to `#SBATCH -p defq`
+    clusterOptions = '--account=DESIM'  // maps to `#SBATCH -A DESIM`
 }
 
 singularity {

From 0516b1dcec58c263e4507c494e0685bba63f9f5d Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 26 Sep 2025 20:13:46 +0000
Subject: [PATCH 04/17] Instructions to download nextflow

---
 docs/newcastle.md | 34 ++++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index 07a9ca492..fd220a670 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -4,10 +4,36 @@ Configuration for the Newcastle high performance computing (HPC) cluster.
 
 ## Setup
 
-Prior to using nextflow, please follow the instructions on the installing conda.
-< to be completed >
+To install nextflow we first need to get the prequisite java from module avail:
 
-We advise either creating a conda environment containing nextflow, or installing nextflow in your base environment if this is not possible.
+`module load Java/17.0.6`
+
+Then installing Nextflow using the standard install options:
+https://www.nextflow.io/docs/latest/install.html
+
+`curl -s https://get.nextflow.io | bash`
+
+Make Nextflow executable:
+
+`chmod +x nextflow`
+
+Then move Nextflow into an executable path. For example:
+
+`mkdir -p $HOME/bin/`
+`mv nextflow $HOME/bin/`
+
+To ensure this works every time you login to the cluster, put inside your `~/.bash_profile` the java install:
+
+`nano ~/.bash_profile`
+
+Then paste in the line for the java install:
+
+```
+#Java module add v17:
+module load Java/17.0.6
+```
+
+Exit nano with, control-X, then y to save, then enter to confirm
 
 ## Run
 
@@ -17,4 +43,4 @@ To use this profile, simply pass Nextflow the -profile newcastle flag eg.
 nextflow run nf-core/_pipeline_ -profile newcastle --outdir results
 ```
 
-In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) on ecoflow.ucl@gmail.com . We are at UCL, but helped set this up.
+In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) at ecoflow.ucl@gmail.com . We are based at UCL, but helped set up this config, and are happy to help.

From 328c03a3c1b3c1a96588b9f7c374412d5471536b Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 15:55:58 +0100
Subject: [PATCH 05/17] Update Newcastle HPC cluster profile details

Add account flag
---
 conf/newcastle.config | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index 17ec1e842..fb1573a76 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,7 +1,8 @@
 params {
-    config_profile_description = 'Newcastle HPC cluster profile'
-    config_profile_contact = 'Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)'
+    config_profile_description = 'Newcastle comet HPC cluster profile'
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
     config_profile_url = ''
+    account = null
 }
 
 executor {
@@ -13,6 +14,14 @@ process {
     errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
     queue   = 'defq'                    // maps to `#SBATCH -p defq`
     clusterOptions = '--account=DESIM'  // maps to `#SBATCH -A DESIM`
+
+    clusterOptions = {
+        def opts = []
+        if (params.account) {
+          opts << "--account=${params.account}"
+        }
+        return opts.join(' ')
+      }
 }
 
 singularity {

From db53f98c260e0a38dce87b2dd1bad745807ef63b Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 15:56:47 +0100
Subject: [PATCH 06/17] Clarify config parameters in newcastle.config

Added comments to clarify config parameters.
---
 conf/newcastle.config | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index fb1573a76..4dde50e6f 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,8 +1,8 @@
 params {
     config_profile_description = 'Newcastle comet HPC cluster profile'
     config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
-    config_profile_url = ''
-    account = null
+    config_profile_url = '' // Not sure of this
+    account = null   // Could be set up as their user ID by default? $USER?
 }
 
 executor {
@@ -13,7 +13,6 @@ process {
     scratch = true
     errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
     queue   = 'defq'                    // maps to `#SBATCH -p defq`
-    clusterOptions = '--account=DESIM'  // maps to `#SBATCH -A DESIM`
 
     clusterOptions = {
         def opts = []

From e28cf8667cbaf05ec96012df86035b6da7b589d4 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:05:11 +0100
Subject: [PATCH 07/17] Update Newcastle config with new parameters and cleanup

---
 conf/newcastle.config | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index 4dde50e6f..538d5e4bf 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,18 +1,16 @@
 params {
     config_profile_description = 'Newcastle comet HPC cluster profile'
-    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
-    config_profile_url = '' // Not sure of this
-    account = null   // Could be set up as their user ID by default? $USER?
-}
-
-executor {
-    name = 'slurm'
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'   //Can add any other people too here.
+    config_profile_url = '' // Need URL to docs
+    account = System.getenv('USER')   // Or could be set to null
+    max_memory = 256.GB
+    max_cpus   = 32
+    max_time   = 48.h
 }
 
 process {
+    executor = 'slurm'
     scratch = true
-    errorStrategy = { task.exitStatus in [137, 140] ? 'retry' : 'finish' }
-    queue   = 'defq'                    // maps to `#SBATCH -p defq`
 
     clusterOptions = {
         def opts = []
@@ -28,3 +26,11 @@ singularity {
     pullTimeout = '2 h'
     autoMounts = true
 }
+
+cleanup = true
+
+profiles {
+    debug {
+        cleanup = false
+    }
+}

From 9ddbfe0b1fe797a74ff79a2881118aff5430c902 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:09:25 +0100
Subject: [PATCH 08/17] limit queue size

---
 conf/newcastle.config | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index 538d5e4bf..b44a12c59 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -21,6 +21,10 @@ process {
       }
 }
 
+executor {
+    queueSize = 100
+}
+
 singularity {
     enabled = true
     pullTimeout = '2 h'

From b057c813dce520e763a0744c843a4e1436363d1c Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:19:42 +0100
Subject: [PATCH 09/17] Enhance Newcastle HPC configuration documentation

Updated Newcastle HPC configuration documentation with detailed usage notes, installation steps for Java and Nextflow, and troubleshooting tips.
---
 docs/newcastle.md | 121 ++++++++++++++++++++++++++++++++++++----------
 1 file changed, 96 insertions(+), 25 deletions(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index fd220a670..f7e9011d8 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -1,46 +1,117 @@
 # nf-core/configs: Newcastle HPC Configuration
 
-Configuration for the Newcastle high performance computing (HPC) cluster.
+Configuration for the Newcastle University HPC cluster (Slurm scheduler).
+
+## ⚠️ Important usage note
+
+**Do not run Nextflow on the login/head node.**
+
+All nf-core pipelines must be launched **from within a Slurm job** using `sbatch`. Running on the login node can overload shared resources and may result in your job being terminated. See Submit the Job section.
 
 ## Setup
 
-To install nextflow we first need to get the prequisite java from module avail:
+### 1. Load Java
+
+Nextflow requires Java. On Newcastle HPC:
+
+    module load Java/17.0.6
+
+To make this persistent, add it to your `~/.bash_profile`:
+
+    # Load Java for Nextflow
+    module load Java/17.0.6
+
+### 2. Install Nextflow
+
+Install Nextflow using the official method:
+
+    curl -s https://get.nextflow.io | bash
+    chmod +x nextflow
+
+Move it to a directory in your `$PATH`:
+
+    mkdir -p $HOME/bin
+    mv nextflow $HOME/bin/
+
+Ensure `$HOME/bin` is in your `PATH` (add to `~/.bash_profile` if needed):
+
+    export PATH="$HOME/bin:$PATH"
+
+### 3. Container system (Singularity / Apptainer)
+
+nf-core pipelines use containers for reproducibility.
+
+On most HPC systems, **Apptainer (formerly Singularity)** is already installed. Check with:
+
+    module avail apptainer
+
+or:
+
+    module avail singularity
+
+Then load it (example):
+
+    module load Apptainer
+
+If neither is available, contact HPC support.
+
+## Running pipelines
+
+### 1. Create a Slurm submission script
+
+Create a file, e.g. `run_nfcore.sh`:
+
+    #!/bin/bash
+    #SBATCH --job-name=nfcore_run
+    #SBATCH --account=YOUR_ACCOUNT
+    #SBATCH --time=24:00:00
+    #SBATCH --cpus-per-task=4
+    #SBATCH --mem=8G
+
+    module load Java/17.0.6
+    module load Apptainer
+
+    nextflow run nf-core/_pipeline_ \
+      -profile newcastle \
+      --account YOUR_ACCOUNT \
+      --outdir results \
+      -resume
 
-`module load Java/17.0.6`
+### 2. Submit the job
 
-Then installing Nextflow using the standard install options:
-https://www.nextflow.io/docs/latest/install.html
+    sbatch run_nfcore.sh
 
-`curl -s https://get.nextflow.io | bash`
+## Configuration options
 
-Make Nextflow executable:
+### `--account`
 
-`chmod +x nextflow`
+You **must** provide a Slurm account when running:
 
-Then move Nextflow into an executable path. For example:
+    --account YOUR_PROJECT_CODE
 
-`mkdir -p $HOME/bin/`
-`mv nextflow $HOME/bin/`
+This is passed to Slurm as:
 
-To ensure this works every time you login to the cluster, put inside your `~/.bash_profile` the java install:
+    #SBATCH --account=YOUR_PROJECT_CODE
 
-`nano ~/.bash_profile`
+## Example command
 
-Then paste in the line for the java install:
+Inside your Slurm script:
 
-```
-#Java module add v17:
-module load Java/17.0.6
-```
+    nextflow run nf-core/rnaseq \
+      -profile newcastle \
+      --account bioinf_project \
+      --outdir results \
+      -resume
 
-Exit nano with, control-X, then y to save, then enter to confirm
+## Troubleshooting
 
-## Run
+- Jobs fail immediately → check `--account` is valid  
+- Nextflow not found → ensure `$HOME/bin` is in your `PATH`  
+- Container errors → ensure Apptainer module is loaded  
+- Jobs not starting → check Slurm queue limits (`squeue`, `sacct`)  
 
-To use this profile, simply pass Nextflow the -profile newcastle flag eg.
+## Support
 
-```bash
-nextflow run nf-core/_pipeline_ -profile newcastle --outdir results
-```
+For issues with this configuration, please contact:
 
-In case of issues, please feel free to reach out to one of the maintainers (Chris Wyatt or Fernando Duarte) at ecoflow.ucl@gmail.com . We are based at UCL, but helped set up this config, and are happy to help.
+- Chris Wyatt (@chriswyatt1)  Email: ecoflow.ucl@gmail.com  

From 2e22da14cba86f3de0a22a62377728f0d5b888df Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:21:10 +0100
Subject: [PATCH 10/17] Update container system references to Apptainer

Updated documentation to reflect the name change from Singularity to Apptainer and specified its availability on the comet system.
---
 docs/newcastle.md | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index f7e9011d8..985f27723 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -37,24 +37,18 @@ Ensure `$HOME/bin` is in your `PATH` (add to `~/.bash_profile` if needed):
 
     export PATH="$HOME/bin:$PATH"
 
-### 3. Container system (Singularity / Apptainer)
+### 3. Container system (Apptainer)
 
 nf-core pipelines use containers for reproducibility.
 
-On most HPC systems, **Apptainer (formerly Singularity)** is already installed. Check with:
+On comet, **Apptainer (formerly Singularity)** is already installed. Check with:
 
     module avail apptainer
 
-or:
-
-    module avail singularity
-
 Then load it (example):
 
     module load Apptainer
 
-If neither is available, contact HPC support.
-
 ## Running pipelines
 
 ### 1. Create a Slurm submission script

From 58c2636cb9600889ef7024cde3a6eaf70f432525 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:23:45 +0100
Subject: [PATCH 11/17] Add error strategy for task exit status handling as per
 nf-core

For non nf-core running pipelines
---
 conf/newcastle.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index b44a12c59..b8ec4fb5c 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -11,7 +11,7 @@ params {
 process {
     executor = 'slurm'
     scratch = true
-
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     clusterOptions = {
         def opts = []
         if (params.account) {

From 2e597e6e95dd191e59fc6cf42f51a49f98e2efd3 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 16:33:09 +0100
Subject: [PATCH 12/17] Update newcastle.md

---
 docs/newcastle.md | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index 985f27723..21bd6608d 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -87,13 +87,25 @@ This is passed to Slurm as:
 
     #SBATCH --account=YOUR_PROJECT_CODE
 
-## Example command
+## Example command to test nextflow is working (run this command, it should work!)
 
 Inside your Slurm script:
 
-    nextflow run nf-core/rnaseq \
+    nextflow run  nf-core/hello \
+      -profile newcastle,test \
+      --account bioinf_project \
+      --outdir results \
+      -resume
+
+## Example "real" command (will not work, just for demonstration)
+
+    nextflow run  nf-core/rnaseq \
       -profile newcastle \
       --account bioinf_project \
+      --input input_samplesheet.csv \
+      --aligner hisat2 \
+      --fasta mygenome.fasta \
+      --gtf myannotation.gtf \
       --outdir results \
       -resume
 

From c3dea1da6dc9232a75b04bf778f161a14f61e523 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Wed, 18 Mar 2026 17:48:04 +0100
Subject: [PATCH 13/17] Update example command for nextflow

---
 docs/newcastle.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index 21bd6608d..6d132ef04 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -91,7 +91,7 @@ This is passed to Slurm as:
 
 Inside your Slurm script:
 
-    nextflow run  nf-core/hello \
+    nextflow run  nf-core/fetchngs \
       -profile newcastle,test \
       --account bioinf_project \
       --outdir results \

From 5eaec586c45acb96859a9fa37279f90a62c8c73d Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 20 Mar 2026 11:30:33 +0100
Subject: [PATCH 14/17] Update newcastle.config

Added in correct resource limits section
---
 conf/newcastle.config | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index b8ec4fb5c..799c967bb 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,17 +1,19 @@
 params {
     config_profile_description = 'Newcastle comet HPC cluster profile'
-    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'   //Can add any other people too here.
-    config_profile_url = '' // Need URL to docs
-    account = System.getenv('USER')   // Or could be set to null
-    max_memory = 256.GB
-    max_cpus   = 32
-    max_time   = 48.h
+    config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
+    config_profile_url = ''
+    account = System.getenv('USER')
 }
 
 process {
     executor = 'slurm'
     scratch = true
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+    resourceLimits = [
+        memory: 256.GB,
+        cpus: 32,
+        time: 48.h
+    ]
     clusterOptions = {
         def opts = []
         if (params.account) {

From 9ec8ebe79e3ad14bca3cecd80b76b6458cca37eb Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:44:11 +0100
Subject: [PATCH 15/17] Update newcastle.config

Add URL to Newcastle.
Would be better to the actual docs of comet, but this is here for now.
---
 conf/newcastle.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/newcastle.config b/conf/newcastle.config
index 799c967bb..c892d1b55 100644
--- a/conf/newcastle.config
+++ b/conf/newcastle.config
@@ -1,7 +1,7 @@
 params {
     config_profile_description = 'Newcastle comet HPC cluster profile'
     config_profile_contact = 'Chris Wyatt (@chriswyatt1)'
-    config_profile_url = ''
+    config_profile_url = 'https://hpc.researchcomputing.ncl.ac.uk/calc/resources/'
     account = System.getenv('USER')
 }
 

From 142030fb707c5d594af2c2794da2087b8ff6bcdf Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 20 Mar 2026 15:07:11 +0100
Subject: [PATCH 16/17] Update newcastle.md

Add specific that its UK Newcastle University
Pseudonym: University of Newcastle upon Tyne
---
 docs/newcastle.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index 6d132ef04..35dcfe175 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -1,6 +1,6 @@
-# nf-core/configs: Newcastle HPC Configuration
+# nf-core/configs: Newcastle University (UK, Comet) HPC Configuration
 
-Configuration for the Newcastle University HPC cluster (Slurm scheduler).
+Configuration for the University of Newcastle upon Tyne HPC cluster (Slurm scheduler).
 
 ## ⚠️ Important usage note
 

From 65949ea97ab7d21474fb2448564893ead9451c95 Mon Sep 17 00:00:00 2001
From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
Date: Fri, 20 Mar 2026 15:11:17 +0100
Subject: [PATCH 17/17] Update newcastle.md

Add link to official page in docs
---
 docs/newcastle.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/newcastle.md b/docs/newcastle.md
index 35dcfe175..487f9cf3e 100644
--- a/docs/newcastle.md
+++ b/docs/newcastle.md
@@ -2,6 +2,8 @@
 
 Configuration for the University of Newcastle upon Tyne HPC cluster (Slurm scheduler).
 
+Check out the docs [here](https://hpc.researchcomputing.ncl.ac.uk/calc/resources/)
+
 ## ⚠️ Important usage note
 
 **Do not run Nextflow on the login/head node.**