Merge branch 'master' into master

.github/CODEOWNERS

@@ -0,0 +1,109 @@
+**/abims** @lecorguille
+**/adcra** @kalayaneech
+**/alice** @bbartholdy
+**/apollo** @drejom
+**/aws_tower** @ggabernet
+**/awsbatch** @apeltzer
+**/azurebatch** @adamrtalbot
+**/azurebatchdev** @abhi18av
+**/bi** @apeltzer
+**/bigpurple** @tobsecret
+**/binac** @apeltzer
+**/biohpc_gen** @phue
+**/biowulf** @qiyubio
+**/cambridge** @EmelineFavreau
+**/cbe** @phue
+**/ccga_dx** @marchoeppner
+**/ccga_med** @marchoeppner
+**/cedars** @rajewski
+**/ceres** @MillironX
+**/cfc** @FriederikeHanssen
+**/cfc_dev** @FriederikeHanssen
+**/cheaha** @lianov @atrull314
+**/computerome** @marcmtk
+**/crg** @joseespinosa
+**/crick** @chris-cheshire @ChristopherBarrington
+**/crukmi** @sppearce
+**/czbiohub_aws** @olgabot
+**/denbi_qbic** @apeltzer
+**/dkfz** @kubranarci
+**/ebc** @marcel-keller
+**/ebi_codon** @saulpierotti
+**/ebi_codon_slurm** @saulpierotti
+**/eddie** @ameynert
+**/engaging** @PhilPalmer
+**/ethz_euler** @jpadesousa
+**/eva** @jfy133
+**/fgcz** @zajacn
+**/fub_curta** @wassimsalam01
+**/genotoul** @chklopp
+**/genouest** @abretaud
+**/gis** @andreas-wilm
+**/google** @FIXME
+**/googlebatch** @hnawar
+**/googlels** @hnawar
+**/hki** @jfy133
+**/hypatia** @lusacristan
+**/icr_davros** @adrlar
+**/ifb_core** @FIXME
+# **imperial** @FIXME
+# **incliva** @FIXME
+# **ipop_up** @FIXME
+# **janelia** @FIXME
+**/jax** @flynnb
+# **ku_sund_dangpu** @FIXME
+# **leicester** @FIXME
+**/lugh** @BarryDigby
+**/maestro** @pierrespc
+# **mana** @FIXME
+# **marvin** @FIXME
+# **medair** @FIXME
+**/mjolnir_globe** @ashildv
+**/mpcdf** @jfy133
+**/munin** @praveenraj2018 @maxulysse
+**/nci_gadi** @mattdton
+**/nu_genomics** @RoganGrant @NUjon
+# **oist** @FIXME
+**/pasteur** @rplanel
+**/pawsey_nimbus** @marcodelapierre @SarahBeecroft
+**/pawsey_setonix** @georgiesamaha @SarahBeecroft
+**/pdc_kth** @pontus
+**/phoenix** @apeltzer
+**/uppmax** @ewels @MaxUlysse
+**/demultiplex** @nf-core/demultiplex
+**/azurebatch_pools_Edv4** @vsmalladi
+# **icr_davros** @FIXME
+**/hasta** @sofstam
+**/psmn** @l-modolo
+**/rosalind** @theoportlock
+**/rosalind_uge** @gregorysprenger
+**/sage** @BrunoGrandePhD
+# **sahmri** @FIXME
+**/ilifu** @pvanheus
+**/sanger** @priyanka-surana
+# **scw** @FIXME
+**/seawulf** @davidecarlson
+**/seg_globe** @ashildv
+**/software_license** @maxulysse
+**/tigem** @giusmar
+**/tubingen_apg** @sc13-bioinf
+# **tuos_stanage** @FIXME
+**/ucd_sonic** @brucemoran
+# **ucl_myriad** @FIXME
+**/uct_hpc** @kviljoen
+**/uge** @gregorysprenger
+**/unc_lccc** @alanhoyle
+**/unc_longleaf** @ahepperla
+# **unibe_ibu** @FIXME
+# **/uod_hpc** @FIXME
+**/utd_ganymede** @edmundmiller @alyssa-ab
+**/uw_hyak_pedslabs** @CarsonJM
+**/uzh** @apeltzer
+**/vai** @njspix
+# **/vsc_kul_uhasselt** @FIXME
+**/vsc_ugent** @nvnieuwk @matthdsm
+**/wcm** @DoaneAS
+# **/wehi** @FIXME
+# **/wustl_htcf** @FIXME
+# **/xanadu** @FIXME
+**/tufts** @zhan4429

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Steps for adding a new config profile:
 - [ ] Add your profile name to the `profile:` scope in `.github/workflows/main.yml`
 
 <!--
-If you require/still waiting for a review, please feel free to request from @nf-core/configs-team
+If you require/still waiting for a review, please feel free to request a review from @nf-core/maintainers
 
 Please see uploading to`nf-core/configs` for more details:
 https://github.com/nf-core/configs#uploading-to-nf-coreconfigs

.github/generate_codeowners.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+CONFIGS=$(fd . -e .config 'conf/')
+
+output_file=".github/CODEOWNERS"
+rm $output_file
+
+for file in $CONFIGS; do
+    # Get the line of the file that starts with config_profile_contact
+    line=$(rg "config_profile_contact" "$file")
+    # and then get the username after the @ and remove anything after it
+    username=$(echo "$line" | sed 's/^.*@/@/g')
+    # Remove the )'
+    username=$(echo "$username" | sed 's/).*$//g')
+
+    # Get the insitute name
+    # conf/<institute>.config
+    institute=$(echo "$file" | sed 's/^.*\///g' | sed 's/\.config$//g')
+
+    # # Remove quotes from authors
+    echo "**$institute**" $username >> $output_file
+done

.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 "[email protected]"
           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.yml

@@ -1,22 +1,21 @@
-name: Code Linting
+name: Lint tools code formatting
 on:
-  pull_request:
   push:
     branches:
       - master
+  pull_request:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  prettier:
+  pre-commit:
     runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v2
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v2
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: pre-commit/[email protected]

.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