Fix/bclconvert gcp

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.nf-core.yml

@@ -27,7 +27,7 @@ lint:
   template_strings:
     - bin/cmgg_genelists
   nf_test_content: false
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: Matthias De Smet, Nicolas Vannieuwkerke

.prettierignore

@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

conf/modules.config

@@ -14,13 +14,14 @@ process {
 
     // BCL convert
     withName: BCLCONVERT {
+        cpus       = 32
+        memory     = 128.GB
+        disk       = { 500.GB * task.attempt }
         ext.args   = {
             [
                 meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
                 "--force",
-                "--bcl-num-parallel-tiles ${task.cpus}",
-                "--bcl-num-conversion-threads ${task.cpus}",
-                "--bcl-num-compression-threads ${task.cpus}",
+                "--strict",
             ].join(" ").trim()
         }
     }