Merge branch 'master' into eva-java-correction

.github/workflows/fix-linting.yml

@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/configs'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push

.github/workflows/main.yml

@@ -66,6 +66,7 @@ jobs:
           - "jax"
           - "lugh"
           - "marvin"
+          - "mjolnir_globe"
           - "maestro"
           - "mpcdf"
           - "munin"

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)

conf/mjolnir_globe.config

@@ -0,0 +1,25 @@
+//Profile config names for nf-core/configs
+params {
+  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/'
+  max_memory = 500.GB
+  max_cpus = 50
+  max_time = 720.h
+}
+
+singularity {
+        enabled = true
+        autoMounts = true
+        cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity'
+}
+        
+process {
+ executor = 'slurm'
+}
+        
+cleanup = true
+       
+executor {
+  queueSize = 10
+}

conf/vsc_ugent.config

@@ -1,8 +1,11 @@
+// Define the Scratch directory
+def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
+
 // Specify the work directory
-workDir = "$VSC_SCRATCH_VO_USER/work"
+workDir = "$scratch_dir/work"
 
 // Perform work directory cleanup when the run has succesfully completed
-cleanup = true
+// cleanup = true
 
 // Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
 executor {
@@ -13,7 +16,7 @@ executor {
 singularity {
     enabled = true
     autoMounts = true
-    cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
+    cacheDir = "$scratch_dir/singularity"
 }
 
 // Define profiles for each cluster
@@ -32,8 +35,8 @@ profiles {
             executor = 'slurm'
             queue = 'skitty'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -51,8 +54,8 @@ profiles {
             executor = 'slurm'
             queue = 'swalot'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -70,8 +73,8 @@ profiles {
             executor = 'slurm'
             queue = 'victini'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -89,8 +92,8 @@ profiles {
             executor = 'slurm'
             queue = 'kirlia'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 
@@ -108,8 +111,8 @@ profiles {
             executor = 'slurm'
             queue = 'doduo'
             maxRetries = 2
-            beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
-            scratch = "$VSC_SCRATCH_VO_USER"
+            beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
+            scratch = "$scratch_dir"
         }
     }
 }

docs/mjolnir_globe.md

@@ -0,0 +1,31 @@
+# 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.
+
+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.
+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_nfcore
+
+# nextflow - limiting memory of virtual java machine
+NXF_OPTS='-Xms1g -Xmx4g'
+```
+
+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 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
+module purge
+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.
+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.

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" }