From fdac67afbf784486fa38d4988d19865c455e9d22 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Tue, 31 Aug 2021 13:58:39 +0200
Subject: [PATCH 01/25] Create computerome.config

---
 conf/computerome.config | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 conf/computerome.config

diff --git a/conf/computerome.config b/conf/computerome.config
new file mode 100644
index 0000000..1085b49
--- /dev/null
+++ b/conf/computerome.config
@@ -0,0 +1,26 @@
+singularityDir = "/gpfs/scratch/${USER}/singularity_images_nextflow"
+
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Computerome 2.0 cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
+  config_profile_url = 'https://www.computerome.dk/'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = singularityDir
+}
+
+process {
+  beforeScript = 'module load singularity squashfs-tools'
+  executor = 'pbs'
+  queue = { task.memory >= 192.GB ? 'fatnode': 'thinnode'}
+}
+
+params {
+  max_memory = 1500.GB
+  max_cpus = 40
+  max_time = 168.h
+}

From aad24862158637f014052dce10a7f25b995d5541 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Tue, 31 Aug 2021 14:10:19 +0200
Subject: [PATCH 02/25] Create computerome.md

---
 docs/computerome.md | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 docs/computerome.md

diff --git a/docs/computerome.md b/docs/computerome.md
new file mode 100644
index 0000000..64b2e4c
--- /dev/null
+++ b/docs/computerome.md
@@ -0,0 +1,7 @@
+# nf-core/configs: Computerome 2.0 Configuration
+
+This is a first attempt at creating a profile for the Computerome 2.0 cluster.
+
+To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
+
+>NB: You will need an account to use the HPC cluster Computerome in order to run the pipeline. If in doubt contact IT.

From a641284533a3f81f1462493f4a2e18ee958a3dc9 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Tue, 31 Aug 2021 14:12:24 +0200
Subject: [PATCH 03/25] Update nfcore_custom.config

Add computerome to profiles
---
 nfcore_custom.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nfcore_custom.config b/nfcore_custom.config
index 99a31e4..2b5eca1 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -23,6 +23,7 @@ profiles {
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
+  computerome  { includeConfig "${params.custom_config_base}/conf/computerome.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }

From e576b1a7ddcad47d5e1bb26700dc737bb144d074 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Tue, 31 Aug 2021 14:32:56 +0200
Subject: [PATCH 04/25] Update README.md

Add computerome
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 948b714..fe6e8cb 100644
--- a/README.md
+++ b/README.md
@@ -102,6 +102,7 @@ Currently documentation is available for the following systems:
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
 * [CFC](docs/cfc.md)
+* [Computerome](docs/computerome.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [DENBI_QBIC](docs/denbi_qbic.md)

From 06632d541db5a19a8a4dc910fef0ae039257da95 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Tue, 31 Aug 2021 14:35:24 +0200
Subject: [PATCH 05/25] Update main.yml

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 12d23f0..f8036fe 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -30,6 +30,7 @@ jobs:
             - 'ccga_med'
             - 'cfc'
             - 'cfc_dev'
+            - 'computerome'
             - 'crick'
             - 'denbi_qbic'
             - 'ebc'

From d4c71f0d8d3a4bfceec0fcf08174868e6163b19c Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 1 Sep 2021 13:22:31 +0200
Subject: [PATCH 06/25] Update computerome.config

---
 conf/computerome.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 1085b49..ef9e71f 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -1,4 +1,4 @@
-singularityDir = "/gpfs/scratch/${USER}/singularity_images_nextflow"
+singularityDir = "/scratch/${USER}/singularity_images_nextflow"
 
 //Profile config names for nf-core/configs
 params {
@@ -14,7 +14,7 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load singularity squashfs-tools'
+  beforeScript = 'module load tools singularity/3.8.0'
   executor = 'pbs'
   queue = { task.memory >= 192.GB ? 'fatnode': 'thinnode'}
 }

From a1413ce18ee2cdc0e4b97a0d66b89f632249c5aa Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 1 Sep 2021 21:47:48 +0200
Subject: [PATCH 07/25] Update computerome.config

---
 conf/computerome.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index ef9e71f..1e64c3d 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -16,7 +16,6 @@ singularity {
 process {
   beforeScript = 'module load tools singularity/3.8.0'
   executor = 'pbs'
-  queue = { task.memory >= 192.GB ? 'fatnode': 'thinnode'}
 }
 
 params {

From e2d54cb56c579d5a3467d66a3d9a39f59b577017 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 1 Sep 2021 22:06:56 +0200
Subject: [PATCH 08/25] Update computerome.config

---
 conf/computerome.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 1e64c3d..92e2efc 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -1,5 +1,3 @@
-singularityDir = "/scratch/${USER}/singularity_images_nextflow"
-
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Computerome 2.0 cluster profile provided by nf-core/configs.'
@@ -10,7 +8,6 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = singularityDir
 }
 
 process {

From 1bf2d436d48192b47020bb2ee3de76bca0d6a627 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 1 Sep 2021 22:21:31 +0200
Subject: [PATCH 09/25] Update computerome.config

---
 conf/computerome.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/computerome.config b/conf/computerome.config
index 92e2efc..c789b48 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -8,6 +8,7 @@ params {
 singularity {
   enabled = true
   autoMounts = true
+  cacheDir = './scratch'
 }
 
 process {

From 84f94d92c4c2d39a7ddf2095cf48dc3c30e4a8dd Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Fri, 10 Sep 2021 15:10:19 +0200
Subject: [PATCH 10/25] Update computerome.config

Added a way to use `--project` to provide project information to the scheduler. Inspired by the uppmax config
---
 conf/computerome.config | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index c789b48..97ee866 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -3,17 +3,19 @@ params {
   config_profile_description = 'Computerome 2.0 cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
+  project = null
 }
 
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = './scratch'
+  cacheDir = { "/home/projects/$params.project/scratch" }
 }
 
 process {
-  beforeScript = 'module load tools singularity/3.8.0'
+  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=/home/projects/$params.project/scratch" }
   executor = 'pbs'
+  clusterOptions = { "-A $params.project -W group_list=$params.project" }
 }
 
 params {

From f46172c25b9cb2d3058a07d684bb0113e9dd0caa Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 08:16:11 +0200
Subject: [PATCH 11/25] Update computerome.md

Update with usage, heavily inspired by the UPPMAX docs
---
 docs/computerome.md | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/docs/computerome.md b/docs/computerome.md
index 64b2e4c..dffd059 100644
--- a/docs/computerome.md
+++ b/docs/computerome.md
@@ -4,4 +4,27 @@ This is a first attempt at creating a profile for the Computerome 2.0 cluster.
 
 To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
 
->NB: You will need an account to use the HPC cluster Computerome in order to run the pipeline. If in doubt contact IT.
+## Using the Computerome config profile
+
+Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
+
+To use, run the pipeline with `-profile computerome` (one hyphen).
+This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome servers.
+It will enable `Nextflow` to manage the pipeline jobs via the `Torque` job scheduler.
+Using this profile, `Singularity` image(s) containing required software(s) will be downloaded before execution of the pipeline.
+
+Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. The computerome configuration uses your project's scratch folder as the cachedir if not specified.
+
+In addition to this config profile, you will also need to specify a Computerome project id.
+You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
+For example:
+
+```bash
+# Launch a nf-core pipeline with the computerome profile for the project id ab00002
+$ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]
+```
+
+> NB: If you're not sure what your Computerome project ID is, try running `groups`.
+
+Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
+Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.

From a0ba05fd991630e2e2d9de88d85c9be478120ec7 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 08:36:30 +0200
Subject: [PATCH 12/25] Update computerome.config

---
 conf/computerome.config | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 97ee866..5445540 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,6 +4,10 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
+  
+  max_memory = 1500.GB
+  max_cpus = 40
+  max_time = 168.h
 }
 
 singularity {
@@ -17,9 +21,3 @@ process {
   executor = 'pbs'
   clusterOptions = { "-A $params.project -W group_list=$params.project" }
 }
-
-params {
-  max_memory = 1500.GB
-  max_cpus = 40
-  max_time = 168.h
-}

From cf899a2a4e55c800a15c38509f78ddfb1ef7c60b Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 08:48:27 +0200
Subject: [PATCH 13/25] Update computerome.md

---
 docs/computerome.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/computerome.md b/docs/computerome.md
index dffd059..1195445 100644
--- a/docs/computerome.md
+++ b/docs/computerome.md
@@ -28,3 +28,13 @@ $ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]
 
 Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
 Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
+
+## About Computerome 2.0
+
+The Danish National Supercomputer for Life Sciences (a.k.a. Computerome) is installed at the DTU National Lifescience Center at Technical University of Denmark.
+
+The computer hardware is funded with grants from Technical University of Denmark (DTU), University of Copenhagen (KU) and Danish e-infrastructure Cooperation (DeiC) - also, it is the official Danish ELIXIR Node.
+
+Computerome 1.0 was opened in November 2014 at #121 on TOP500 Supercomputing Sites.
+
+The current setup, Computerome 2.0, was opened in 2019. It's compute resources consists of 31760 CPU cores with 210 TeraBytes of memory, connected to 17 PetaBytes of High-performance storage,

From 0327ef40ea6093d501c488c45c92d893048074c4 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 13:20:57 +0200
Subject: [PATCH 14/25] Update computerome.config

---
 conf/computerome.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 5445540..9b524b9 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -5,9 +5,9 @@ params {
   config_profile_url = 'https://www.computerome.dk/'
   project = null
   
-  max_memory = 1500.GB
+  max_memory = 1500.GB #Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_cpus = 40
-  max_time = 168.h
+  max_time = 168.h #There is no max walltime on the cluster, but a week seems sensible if not directly specified
 }
 
 singularity {
@@ -19,5 +19,6 @@ singularity {
 process {
   beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=/home/projects/$params.project/scratch" }
   executor = 'pbs'
+  queueSize = 2000
   clusterOptions = { "-A $params.project -W group_list=$params.project" }
 }

From e5cba18c9ba9b890fd57a7c74729a3b484973f99 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 13:28:33 +0200
Subject: [PATCH 15/25] Update computerome.config

---
 conf/computerome.config | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 9b524b9..0d12191 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -5,9 +5,12 @@ params {
   config_profile_url = 'https://www.computerome.dk/'
   project = null
   
-  max_memory = 1500.GB #Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
+  //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
+  max_memory = 1500.GB 
   max_cpus = 40
-  max_time = 168.h #There is no max walltime on the cluster, but a week seems sensible if not directly specified
+  
+  //There is no max walltime on the cluster, but a week seems sensible if not directly specified
+  max_time = 168.h 
 }
 
 singularity {
@@ -21,4 +24,4 @@ process {
   executor = 'pbs'
   queueSize = 2000
   clusterOptions = { "-A $params.project -W group_list=$params.project" }
-}
+} 

From 2e515dc861d3753a792bedc43fa59655b4c51931 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 13:38:25 +0200
Subject: [PATCH 16/25] Update computerome.config

Don't raise an error when --project is specified
---
 conf/computerome.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/computerome.config b/conf/computerome.config
index 0d12191..f413d79 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,6 +4,7 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
+  params.schema_ignore_params = "project"
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 

From 1071eb9d2e2148cef651718eed591cea305a1f11 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 13:38:46 +0200
Subject: [PATCH 17/25] Update computerome.config

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

diff --git a/conf/computerome.config b/conf/computerome.config
index f413d79..34b1121 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,7 +4,7 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
-  params.schema_ignore_params = "project"
+  schema_ignore_params = "project"
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 

From 8ebdd438983d6da6ddd5cba27fda07c67b5742a2 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 14:01:35 +0200
Subject: [PATCH 18/25] Update computerome.config

---
 conf/computerome.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 34b1121..e4f41e8 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -5,6 +5,7 @@ params {
   config_profile_url = 'https://www.computerome.dk/'
   project = null
   schema_ignore_params = "project"
+  singularity_cache_dir = { "/home/projects/$params.project/scratch" }
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 
@@ -17,7 +18,7 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = { "/home/projects/$params.project/scratch" }
+  cacheDir = params.singularity_cache_dir
 }
 
 process {

From 366f945a401def16bafb2a1e0d0713824f23fe4a Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 14:20:55 +0200
Subject: [PATCH 19/25] Update computerome.config

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

diff --git a/conf/computerome.config b/conf/computerome.config
index e4f41e8..aaa8d5b 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -5,7 +5,7 @@ params {
   config_profile_url = 'https://www.computerome.dk/'
   project = null
   schema_ignore_params = "project"
-  singularity_cache_dir = { "/home/projects/$params.project/scratch" }
+  cache = { "/home/projects/$params.project/scratch" }
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 
@@ -18,11 +18,11 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = params.singularity_cache_dir
+  cacheDir = params.cache
 }
 
 process {
-  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=/home/projects/$params.project/scratch" }
+  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache; export NXF_SINGULARITY_CACHEDIR=$params.cache" }
   executor = 'pbs'
   queueSize = 2000
   clusterOptions = { "-A $params.project -W group_list=$params.project" }

From 275288632da34cb02b409255b5fd9ed0156d99ef Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 14:22:22 +0200
Subject: [PATCH 20/25] Update computerome.config

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

diff --git a/conf/computerome.config b/conf/computerome.config
index aaa8d5b..d047bdb 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -5,7 +5,7 @@ params {
   config_profile_url = 'https://www.computerome.dk/'
   project = null
   schema_ignore_params = "project"
-  cache = { "/home/projects/$params.project/scratch" }
+  cache_dir = { "/home/projects/$params.project/scratch" }
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 
@@ -18,11 +18,11 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = params.cache
+  cacheDir = params.cache_dir
 }
 
 process {
-  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache; export NXF_SINGULARITY_CACHEDIR=$params.cache" }
+  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir; export NXF_SINGULARITY_CACHEDIR=$params.cache_dir" }
   executor = 'pbs'
   queueSize = 2000
   clusterOptions = { "-A $params.project -W group_list=$params.project" }

From 86e21b378ae8d8e32f9537fa4c05b71ace112139 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Mon, 13 Sep 2021 14:26:10 +0200
Subject: [PATCH 21/25] Update computerome.config

---
 conf/computerome.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index d047bdb..8a451a6 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,8 +4,7 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
-  schema_ignore_params = "project"
-  cache_dir = { "/home/projects/$params.project/scratch" }
+  schema_ignore_params = "project,genomes,cache_dir,modules"
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 
@@ -14,6 +13,7 @@ params {
   //There is no max walltime on the cluster, but a week seems sensible if not directly specified
   max_time = 168.h 
 }
+params.cache_dir = { "/home/projects/$params.project/scratch" }
 
 singularity {
   enabled = true

From 29003e13f1289db0e0acb6201c88640c54dea81e Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 15 Sep 2021 10:22:57 +0200
Subject: [PATCH 22/25] Update computerome.config

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

diff --git a/conf/computerome.config b/conf/computerome.config
index 8a451a6..7cc0d2e 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -13,7 +13,7 @@ params {
   //There is no max walltime on the cluster, but a week seems sensible if not directly specified
   max_time = 168.h 
 }
-params.cache_dir = { "/home/projects/$params.project/scratch" }
+params.cache_dir = "/home/projects/$params.project/scratch"
 
 singularity {
   enabled = true
@@ -22,8 +22,8 @@ singularity {
 }
 
 process {
-  beforeScript = { "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir; export NXF_SINGULARITY_CACHEDIR=$params.cache_dir" }
+  beforeScript = "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir"
   executor = 'pbs'
   queueSize = 2000
-  clusterOptions = { "-A $params.project -W group_list=$params.project" }
+  clusterOptions = "-A $params.project -W group_list=$params.project"
 } 

From 9a8644ef436b61484efd5d5598f9c1adfe14741b Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 15 Sep 2021 11:10:02 +0200
Subject: [PATCH 23/25] Update computerome.md

---
 docs/computerome.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/computerome.md b/docs/computerome.md
index 1195445..b2e624f 100644
--- a/docs/computerome.md
+++ b/docs/computerome.md
@@ -1,7 +1,5 @@
 # nf-core/configs: Computerome 2.0 Configuration
 
-This is a first attempt at creating a profile for the Computerome 2.0 cluster.
-
 To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
 
 ## Using the Computerome config profile

From ab8a9ad0b89f00f08c13e6bc20b4f8f40c4c47d6 Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 15 Sep 2021 13:27:23 +0200
Subject: [PATCH 24/25] Update computerome.config

---
 conf/computerome.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 7cc0d2e..1683900 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,7 +4,7 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
-  schema_ignore_params = "project,genomes,cache_dir,modules"
+  schema_ignore_params = "project,cache_dir"
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
   max_memory = 1500.GB 
@@ -12,8 +12,9 @@ params {
   
   //There is no max walltime on the cluster, but a week seems sensible if not directly specified
   max_time = 168.h 
+  
+  cache_dir = "/home/projects/$params.project/scratch"
 }
-params.cache_dir = "/home/projects/$params.project/scratch"
 
 singularity {
   enabled = true

From 8b29b5584ed8a94aecc27507a03d0ef7ce58511d Mon Sep 17 00:00:00 2001
From: Marc Trunjer Kusk Nielsen <marc.mtk@gmail.com>
Date: Wed, 15 Sep 2021 14:20:02 +0200
Subject: [PATCH 25/25] Update computerome.config

---
 conf/computerome.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/conf/computerome.config b/conf/computerome.config
index 1683900..1411127 100644
--- a/conf/computerome.config
+++ b/conf/computerome.config
@@ -4,6 +4,7 @@ params {
   config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
   config_profile_url = 'https://www.computerome.dk/'
   project = null
+  cache_dir = "/home/projects/$params.project/scratch"
   schema_ignore_params = "project,cache_dir"
   
   //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
@@ -12,8 +13,6 @@ params {
   
   //There is no max walltime on the cluster, but a week seems sensible if not directly specified
   max_time = 168.h 
-  
-  cache_dir = "/home/projects/$params.project/scratch"
 }
 
 singularity {