Merge branch 'master' into master

.github/workflows/fix-linting.yml

@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # 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/') &&
@@ -13,43 +13,77 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # 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
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # 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 pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         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 commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/configs/actions/runs/${{ github.run_id }}) for more details.

.github/workflows/linting_comment.yml

@@ -0,0 +1,28 @@
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork {%- raw %}
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        with:
+          workflow: linting.yml
+          workflow_conclusion: completed
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md

.github/workflows/main.yml

@@ -2,6 +2,11 @@ name: Configs tests
 
 on: [pull_request, push]
 
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test_all_profiles:
     runs-on: ubuntu-latest
@@ -153,9 +158,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "latest-everything"
       - name: Check ${{ matrix.profile }} profile
         env:
           SCRATCH: "~"

conf/incliva.config

@@ -13,31 +13,28 @@ def getHostname() {
 }
 
 // Function to set singularity path according to which host nextflow is running on
-def setHostConfig(String hostname) {
-    if (hostname == 'vlinuxcervantes3srv') {
-        System.out.println("\nINFO: working on ${hostname}\n")
-
-        // Resources details
-        params.max_memory = 60.GB
-        params.max_cpus = 15
-        singularity.cacheDir =  "/nfs/home/software/singularity/nf_cacheDir"
-
-    } else if (hostname == 'vlinuxcervantes4srv') {
-        System.out.println("\nINFO: working on ${hostname}.\n")
-
-        // Resources details
-        params.max_memory = 120.GB
-        params.max_cpus = 19
-        singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
-
-    } else {
-        System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
-    }
-}
 
-def hostname = getHostname()
+def hostname = { getHostname() }
+
+if (hostname == 'vlinuxcervantes3srv') {
+    System.out.println("\nINFO: working on ${hostname}\n")
+
+    // Resources details
+    params.max_memory = 60.GB
+    params.max_cpus = 15
+    singularity.cacheDir =  "/nfs/home/software/singularity/nf_cacheDir"
 
-setHostConfig(hostname)
+} else if (hostname == 'vlinuxcervantes4srv') {
+    System.out.println("\nINFO: working on ${hostname}.\n")
+
+    // Resources details
+    params.max_memory = 120.GB
+    params.max_cpus = 19
+    singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
+
+} else {
+    System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
+}
 
 // Singularity details
 singularity {

conf/vsc_calcua.config

@@ -10,17 +10,12 @@ workDir = "$scratch_dir/work"
 // Perform work directory cleanup when the run has succesfully completed.
 cleanup = true
 
-// Define function to check if the host machine is the VSC CalcUA.
-// Used to skip various steps in this config during github actions.
-def host_is_calcua() {
-    def host = System.getenv("VSC_INSTITUTE")
-    return ( host == "antwerpen" ) ? true : false
-}
+def host = System.getenv("VSC_INSTITUTE")
 
 // Check if APPTAINER_TMPDIR/SINGULARITY_TMPDIR environment variables are set.
 // If they are available, try to create the tmp directory at the specified location.
 // Skip if host is not CalcUA to avoid hindering github actions.
-if ( host_is_calcua() ) {
+if ( host == "antwerpen" ) {
     def apptainer_tmpdir = System.getenv("APPTAINER_TMPDIR") ?: System.getenv("SINGULARITY_TMPDIR") ?: null
     if (! apptainer_tmpdir ) {
         def tmp_dir = System.getenv("TMPDIR") ?: "/tmp"
@@ -29,10 +24,10 @@ if ( host_is_calcua() ) {
     } else {
         apptainer_tmpdir = new File(apptainer_tmpdir)
         if (! apptainer_tmpdir.exists() ) {
-            dir_created = apptainer_tmpdir.mkdirs()
-            if (! dir_created ) {
+            try {
+                dir_created = apptainer_tmpdir.mkdirs()
+            } catch (java.io.IOException e) {
                 System.err.println("\nWARNING: Could not create directory at the location specified by APPTAINER_TMPDIR/SINGULARITY_TMPDIR: $apptainer_tmpdir\nPlease check if this is a valid path to which you have write permission. Exiting...\n")
-                System.exit(1)
             }
         }
     }
@@ -44,17 +39,23 @@ if ( host_is_calcua() ) {
 // warn the user.
 def partition_checker(String profile) {
     // Skip check if host machine is not CalcUA, in order to not hinder github actions.
-    if (! host_is_calcua() ) {
+    if ( host != "antwerpen" ) {
         // System.err.println("\nWARNING: Skipping comparison of current partition and requested profile because the current machine is not VSC CalcUA.")
         return
     }
+
     def current_partition = System.getenv("SLURM_JOB_PARTITION")
-    if (! current_partition) {
+
+    try {
+        current_partition
+    } catch (java.io.IOException e) {
         System.err.println("\nWARNING: Current partition could not be found in the expected \$SLURM_JOB_PARTITION environment variable. Please make sure that you submit your pipeline via a Slurm job instead of running the nextflow command directly on a login node.\nExiting...\n")
-        System.exit(1)
-    } else if ( current_partition != profile) {
+    }
+
+    try {
+        current_partition = profile
+    } catch (java.io.IOException e) {
         System.err.println("\nWARNING: Slurm job was launched on the \'$current_partition\' partition, but the selected nextflow profile points to the $profile partition instead ('${profile}_local'). When using one of the local node execution profiles, please launch the job on the corresponding partition in Slurm.\nE.g., Slurm job submission command:\n    sbatch --account <project_account> --partition=broadwell script.slurm\nand job script containing a nextflow command with matching profile section:\n    nextflow run <pipeline> -profile vsc_calcua,broadwell_local\nExiting...\n")
-        System.exit(1)
     }
 }
 

conf/wustl_htcf.config

@@ -1,6 +1,16 @@
 // Forked from https://github.com/nf-core/configs/blob/master/conf/prince.config
 
-def singularityDir = set_singularity_path()
+def labEnvVar = System.getenv("LAB")
+
+if (labEnvVar) {
+    System.out.println("Lab: " + labEnvVar)
+    singularityDir = "/ref/$LAB/data/singularity_images_nextflow" // If $LAB is set, use that
+} else {
+    def id = "id -nG".execute().text
+    def labAutodetect = id.split(" ").last()
+    System.out.println("Lab: " + labAutodetect)
+    singularityDir = "/ref/" + labAutodetect + "/data/singularity_images_nextflow"
+}
 
 params {
     config_profile_description  = """
@@ -29,15 +39,3 @@ process {
     beforeScript = "exec \$( spack load --sh singularity )"
     executor     = "slurm"
 }
-
-def set_singularity_path() {
-    def labEnvVar = System.getenv("LAB")
-    if (labEnvVar) {
-        System.out.println("Lab: " + labEnvVar)
-        return "/ref/$LAB/data/singularity_images_nextflow" // If $LAB is set, use that
-    }
-    def id = "id -nG".execute().text
-    def labAutodetect = id.split(" ").last()
-    System.out.println("Lab: " + labAutodetect)
-    return "/ref/" + labAutodetect + "/data/singularity_images_nextflow"
-}