From d3e5c79fb4464c89e1bb54cab12be484446d0506 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 20 May 2022 15:44:20 +0200
Subject: [PATCH 01/19] Create holo_globe

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

diff --git a/conf/holo_globe b/conf/holo_globe
new file mode 100644
index 0000000..f10bcd8
--- /dev/null
+++ b/conf/holo_globe
@@ -0,0 +1,26 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - seg_globe profile provided by nf-core/configs.'
+  config_profile_contact = 'Aashild Vaagene (@ashildv)'
+  config_profile_url = 'https://globe.ku.dk/research/evogenomics/'
+  max_memory = 250.GB
+  max_cpus = 35
+  max_time = 720.h
+}
+
+//singularity {
+//  enabled = true
+//  autoMounts = true
+// cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity'
+//}
+
+process {
+ executor = 'slurm'
+ queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' }
+}
+        
+cleanup = true
+       
+executor {
+  queueSize = 8
+}

From bb25c77e7c19fb7a427cba000469f333dd0b5db7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 20 May 2022 17:01:30 +0200
Subject: [PATCH 02/19] Update holo_globe

---
 conf/holo_globe | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/holo_globe b/conf/holo_globe
index f10bcd8..8d4d6c1 100644
--- a/conf/holo_globe
+++ b/conf/holo_globe
@@ -8,6 +8,12 @@ params {
   max_time = 720.h
 }
 
+conda {
+   enabled=true
+   cacheDir = '/maps/projects/mjolnir1/people/prj558/cache/conda'
+}
+    
+
 //singularity {
 //  enabled = true
 //  autoMounts = true

From 0b51552e88c090c8d48ac1dcd234e2d794ec0042 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Tue, 31 May 2022 15:23:43 +0200
Subject: [PATCH 03/19] Update holo_globe

---
 conf/holo_globe | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/conf/holo_globe b/conf/holo_globe
index 8d4d6c1..3f42ad7 100644
--- a/conf/holo_globe
+++ b/conf/holo_globe
@@ -1,28 +1,30 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - seg_globe profile provided by nf-core/configs.'
+  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - holo_globe profile provided by nf-core/configs.'
   config_profile_contact = 'Aashild Vaagene (@ashildv)'
   config_profile_url = 'https://globe.ku.dk/research/evogenomics/'
-  max_memory = 250.GB
-  max_cpus = 35
+  max_memory = 500.GB
+  max_cpus = 50
   max_time = 720.h
 }
 
-conda {
-   enabled=true
-   cacheDir = '/maps/projects/mjolnir1/people/prj558/cache/conda'
+singularity {
+        enabled = true
+        autoMounts = true
+        cacheDir = '/maps/projects/mjolnir1/data/cache/nf-eager/singularity'
 }
-    
-
-//singularity {
-//  enabled = true
-//  autoMounts = true
-// cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity'
-//}
 
+env {
+ NXF_SINGULARITY_TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
+ SINGULARITY_TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
+ NXF_OPTS='-Djava.io.tmpdir=/maps/projects/mjolnir1/people/$USER/eager_tmp/ -Xms1g -Xmx4g'
+ TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
+ NXF_TEMP='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
+ SINGULARITY_LOCALCACHEDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
+}
+        
 process {
  executor = 'slurm'
- queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' }
 }
         
 cleanup = true

From 64fe4677b19d6d70e68c14f70e93e4730cb3e2ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Tue, 31 May 2022 15:26:23 +0200
Subject: [PATCH 04/19] Update holo_globe

---
 conf/holo_globe | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/holo_globe b/conf/holo_globe
index 3f42ad7..d8fcd45 100644
--- a/conf/holo_globe
+++ b/conf/holo_globe
@@ -30,5 +30,5 @@ process {
 cleanup = true
        
 executor {
-  queueSize = 8
+  queueSize = 10
 }

From 6d9cc91c5fff21dfc6e0d9f3b2ce64dff44e8d83 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 15:03:47 +0200
Subject: [PATCH 05/19] Update holo_globe

---
 conf/holo_globe | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/conf/holo_globe b/conf/holo_globe
index d8fcd45..3506a1d 100644
--- a/conf/holo_globe
+++ b/conf/holo_globe
@@ -13,15 +13,6 @@ singularity {
         autoMounts = true
         cacheDir = '/maps/projects/mjolnir1/data/cache/nf-eager/singularity'
 }
-
-env {
- NXF_SINGULARITY_TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
- SINGULARITY_TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
- NXF_OPTS='-Djava.io.tmpdir=/maps/projects/mjolnir1/people/$USER/eager_tmp/ -Xms1g -Xmx4g'
- TMPDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
- NXF_TEMP='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
- SINGULARITY_LOCALCACHEDIR='/maps/projects/mjolnir1/people/$USER/eager_tmp/'
-}
         
 process {
  executor = 'slurm'

From 9b9a6f0188b19e635dc5654846555a66e780c7d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 15:09:52 +0200
Subject: [PATCH 06/19] Update and rename holo_globe to mjolnir_globe

---
 conf/{holo_globe => mjolnir_globe} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename conf/{holo_globe => mjolnir_globe} (75%)

diff --git a/conf/holo_globe b/conf/mjolnir_globe
similarity index 75%
rename from conf/holo_globe
rename to conf/mjolnir_globe
index 3506a1d..6aaeea1 100644
--- a/conf/holo_globe
+++ b/conf/mjolnir_globe
@@ -1,8 +1,8 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - holo_globe profile provided by nf-core/configs.'
+  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.'
   config_profile_contact = 'Aashild Vaagene (@ashildv)'
-  config_profile_url = 'https://globe.ku.dk/research/evogenomics/'
+  config_profile_url = 'https://globe.ku.dk/research/hologenomics/'
   max_memory = 500.GB
   max_cpus = 50
   max_time = 720.h

From 2988e33576695923f7ecf832b705789441610e4d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 15:38:07 +0200
Subject: [PATCH 07/19] Create mjolnir_globe.md

---
 docs/mjolnir_globe.md | 46 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 docs/mjolnir_globe.md

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
new file mode 100644
index 0000000..f43056b
--- /dev/null
+++ b/docs/mjolnir_globe.md
@@ -0,0 +1,46 @@
+# nf-core/configs: Section for Hologenomics at GLOBE, Univeristy of Copenhagen (Mjolnir server) Configuration
+
+> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
+
+Prior to runing the pipeline for the first time, users must create a hidden directory called .tmp_eager in their user/work directory where the tmp files from nf-core/eager will be re-directed by the NXF_TEMP command (see below).
+
+```bash
+#navigate into correct directory
+cd /maps/projects/mjolnir1/people/$USER
+
+#create .tmp_eager directory. This is a hidden directory.
+mkdir .tmp_eager
+```
+
+The contents of the .tmp_eager directory should be periodically deleted to save on space. 
+If the NXF_TEMP command is not used to properly re-direct tmp files the /tmp directory on the compute nodes will be used and quickly filled up, which will make it so that noone can work on these nodes until the files are removed.
+
+The following lines **must** be added by users to their .bash_profile:
+
+```bash
+#re-direct tmp files away from /tmp directories on compute nodes or the headnode
+export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_eager
+
+# nextflow - limiting memory of virtual java machine
+NXF_OPTS='-Xms1g -Xmx4g'
+```
+
+
+The profile is configured to run with Singularity
+
+Before running the pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
+
+```bash
+## Load Java and Nextflow environment modules
+module purge
+module load jdk/1.8.0_291 miniconda/4.9.2 singularity/3.8.0 nextflow/21.04.1.5556
+```
+
+All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
+The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
+
+
+
+This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.
+
+> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.

From 940077190b822f43713d1eda5041937b5216a36b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 15:38:40 +0200
Subject: [PATCH 08/19] Update mjolnir_globe.md

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

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index f43056b..947be25 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -2,7 +2,7 @@
 
 > **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
 
-Prior to runing the pipeline for the first time, users must create a hidden directory called .tmp_eager in their user/work directory where the tmp files from nf-core/eager will be re-directed by the NXF_TEMP command (see below).
+Prior to runing the pipeline for the first time, users **must** create a hidden directory called .tmp_eager in their user/work directory where the tmp files from nf-core/eager will be re-directed by the NXF_TEMP command (see below).
 
 ```bash
 #navigate into correct directory

From e871dc87f9ad572c429450b235a75c61e31200eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 15:59:11 +0200
Subject: [PATCH 09/19] Update mjolnir_globe.md

---
 docs/mjolnir_globe.md | 29 +++++++----------------------
 1 file changed, 7 insertions(+), 22 deletions(-)

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index 947be25..7ccef10 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -2,20 +2,12 @@
 
 > **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
 
-Prior to runing the pipeline for the first time, users **must** create a hidden directory called .tmp_eager in their user/work directory where the tmp files from nf-core/eager will be re-directed by the NXF_TEMP command (see below).
+Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_eager` in their data/project directory on Mjolnir where the temp files from `nf-core/eager` will be re-directed by the `NXF_TEMP` command (see below).
 
-```bash
-#navigate into correct directory
-cd /maps/projects/mjolnir1/people/$USER
+The contents of the `.tmp_eager` directory should be periodically deleted manually to save on space. 
+If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which block anyone from working on these nodes until the offending user removes their files.
 
-#create .tmp_eager directory. This is a hidden directory.
-mkdir .tmp_eager
-```
-
-The contents of the .tmp_eager directory should be periodically deleted to save on space. 
-If the NXF_TEMP command is not used to properly re-direct tmp files the /tmp directory on the compute nodes will be used and quickly filled up, which will make it so that noone can work on these nodes until the files are removed.
-
-The following lines **must** be added by users to their .bash_profile:
+The following lines **must** be added by users to their `~/.bash_profile`:
 
 ```bash
 #re-direct tmp files away from /tmp directories on compute nodes or the headnode
@@ -25,8 +17,7 @@ export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_eager
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
 
-
-The profile is configured to run with Singularity
+Once you have created the `.tmp_eager` directory and added the above lines of code to your `.bash_profile` you can run the pipeline.
 
 Before running the pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
 
@@ -36,11 +27,5 @@ module purge
 module load jdk/1.8.0_291 miniconda/4.9.2 singularity/3.8.0 nextflow/21.04.1.5556
 ```
 
-All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
-The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
-
-
-
-This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.
-
-> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.
+All of the intermediate output files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
+The `mjolnir_globe` config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.

From 0f6fb0c10d23bb385052633307008c02eb863a20 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 16:00:22 +0200
Subject: [PATCH 10/19] Update mjolnir_globe.md

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

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index 7ccef10..3f6beaf 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -5,7 +5,7 @@
 Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_eager` in their data/project directory on Mjolnir where the temp files from `nf-core/eager` will be re-directed by the `NXF_TEMP` command (see below).
 
 The contents of the `.tmp_eager` directory should be periodically deleted manually to save on space. 
-If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which block anyone from working on these nodes until the offending user removes their files.
+If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.
 
 The following lines **must** be added by users to their `~/.bash_profile`:
 

From 7a63e0a2ec6936581607517d00165022d3123991 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 16:05:28 +0200
Subject: [PATCH 11/19] mjolnir_globe config added

---
 nfcore_custom.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nfcore_custom.config b/nfcore_custom.config
index a659638..88e7227 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -49,6 +49,7 @@ profiles {
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }
+  mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   nihbiowulf   { includeConfig "${params.custom_config_base}/conf/nihbiowulf.config" }

From 62dfda810363813f63b5df345c910a688b0ea54b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 16:07:47 +0200
Subject: [PATCH 12/19] add mjolnir_globe md

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

diff --git a/README.md b/README.md
index 72797f9..a68a042 100644
--- a/README.md
+++ b/README.md
@@ -121,6 +121,7 @@ Currently documentation is available for the following systems:
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
 - [MARVIN](docs/marvin.md)
+- [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
 - [MPCDF](docs/mpcdf.md)
 - [MUNIN](docs/munin.md)
 - [NU_GENOMICS](docs/nu_genomics.md)

From 2b67d3aaab44bb4146af486e69b2071a30b4efee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 16:30:35 +0200
Subject: [PATCH 13/19] 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 aa11e4e..ac31dfe 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -66,6 +66,7 @@ jobs:
           - "jax"
           - "lugh"
           - "marvin"
+          - "mjolnir_globe"
           - "maestro"
           - "mpcdf"
           - "munin"

From 1d23ba9264f19aa7b29c33492c02ef11c41c9637 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 2 Jun 2022 16:40:29 +0200
Subject: [PATCH 14/19] change name of tmp dir to .tmp_nfcore

---
 docs/mjolnir_globe.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index 3f6beaf..f22fffd 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -2,24 +2,24 @@
 
 > **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
 
-Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_eager` in their data/project directory on Mjolnir where the temp files from `nf-core/eager` will be re-directed by the `NXF_TEMP` command (see below).
+Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below).
 
-The contents of the `.tmp_eager` directory should be periodically deleted manually to save on space. 
+The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space. 
 If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.
 
 The following lines **must** be added by users to their `~/.bash_profile`:
 
 ```bash
 #re-direct tmp files away from /tmp directories on compute nodes or the headnode
-export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_eager
+export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
 
 # nextflow - limiting memory of virtual java machine
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
 
-Once you have created the `.tmp_eager` directory and added the above lines of code to your `.bash_profile` you can run the pipeline.
+Once you have created the `.tmp_nfcore` directory and added the above lines of code to your `.bash_profile` you can run an nf-core pipeline.
 
-Before running the pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
+Before running a pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
 
 ```bash
 ## Load Java and Nextflow environment modules

From 22ed36a73d57845f097d7b0eb4afc8a62fd49715 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 3 Jun 2022 15:33:58 +0200
Subject: [PATCH 15/19] cacheDir update

---
 conf/mjolnir_globe | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/mjolnir_globe b/conf/mjolnir_globe
index 6aaeea1..0f30313 100644
--- a/conf/mjolnir_globe
+++ b/conf/mjolnir_globe
@@ -1,8 +1,8 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'Section for Hologenomics @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.'
+  config_profile_description = 'Section for Hologenomics and Section for Molecular Ecology and Evolution @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.'
   config_profile_contact = 'Aashild Vaagene (@ashildv)'
-  config_profile_url = 'https://globe.ku.dk/research/hologenomics/'
+  config_profile_url = 'https://globe.ku.dk/research/'
   max_memory = 500.GB
   max_cpus = 50
   max_time = 720.h
@@ -11,7 +11,7 @@ params {
 singularity {
         enabled = true
         autoMounts = true
-        cacheDir = '/maps/projects/mjolnir1/data/cache/nf-eager/singularity'
+        cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity'
 }
         
 process {

From 144ca851c1b663c48c37a3155a8266acaf244581 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 3 Jun 2022 15:36:19 +0200
Subject: [PATCH 16/19] Update mjolnir_globe.md

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

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index f22fffd..b43ae05 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -24,7 +24,7 @@ Before running a pipeline you will need to load Java, Miniconda, Singularity and
 ```bash
 ## Load Java and Nextflow environment modules
 module purge
-module load jdk/1.8.0_291 miniconda/4.9.2 singularity/3.8.0 nextflow/21.04.1.5556
+module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556
 ```
 
 All of the intermediate output files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.

From 2d8221831824194e3140828a4c1aa6ad784035c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 3 Jun 2022 16:42:08 +0200
Subject: [PATCH 17/19] typo

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

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index b43ae05..56c734d 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -1,4 +1,4 @@
-# nf-core/configs: Section for Hologenomics at GLOBE, Univeristy of Copenhagen (Mjolnir server) Configuration
+# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration
 
 > **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
 

From 34feaa8b6b77d30cca3095935395a3dfdab5e499 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 3 Jun 2022 17:08:15 +0200
Subject: [PATCH 18/19] prettier output

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

diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md
index 56c734d..487819a 100644
--- a/docs/mjolnir_globe.md
+++ b/docs/mjolnir_globe.md
@@ -4,7 +4,7 @@
 
 Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below).
 
-The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space. 
+The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space.
 If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.
 
 The following lines **must** be added by users to their `~/.bash_profile`:

From ed526530d244dc27be9d404fb80afa60105a9b90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Fri, 3 Jun 2022 17:15:12 +0200
Subject: [PATCH 19/19] Rename mjolnir_globe to mjolnir_globe.config

---
 conf/{mjolnir_globe => mjolnir_globe.config} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename conf/{mjolnir_globe => mjolnir_globe.config} (100%)

diff --git a/conf/mjolnir_globe b/conf/mjolnir_globe.config
similarity index 100%
rename from conf/mjolnir_globe
rename to conf/mjolnir_globe.config