From 37d3c30d46ff1cafc3c85456c3d3a702680f1908 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 2 Dec 2025 09:34:38 +0100
Subject: [PATCH 1/4] update bcl-convert config for gcp

---
 conf/modules.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 512adf84..750415bc 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -14,13 +14,13 @@ process {
 
     // BCL convert
     withName: BCLCONVERT {
+        cpus       = 32
+        memory     = 64.GB
         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()
         }
     }

From 9c49fb1e8fafc5cf2623a1287076486699bffbac Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 2 Dec 2025 09:48:05 +0100
Subject: [PATCH 2/4] add dynamic disk allocation

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index 750415bc..97089065 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -16,6 +16,7 @@ process {
     withName: BCLCONVERT {
         cpus       = 32
         memory     = 64.GB
+        disk       = { 500.GB * task.attempt }
         ext.args   = {
             [
                 meta.lane ? "--bcl-only-lane ${meta.lane}" : "",

From 2d51974a2fbec03cd3ff97a89ebe09d85f3844b8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 2 Dec 2025 10:17:19 +0100
Subject: [PATCH 3/4] increase mem

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 97089065..8a8a5c50 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -15,7 +15,7 @@ process {
     // BCL convert
     withName: BCLCONVERT {
         cpus       = 32
-        memory     = 64.GB
+        memory     = 128.GB
         disk       = { 500.GB * task.attempt }
         ext.args   = {
             [

From 8d95252a81f599f223a163a38e1b296936307af8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 2 Dec 2025 10:20:12 +0100
Subject: [PATCH 4/4] fix linting

---
 .github/workflows/linting.yml | 6 +++---
 .nf-core.yml                  | 2 +-
 .prettierignore               | 2 ++
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026..7a527a34 100644
--- a/.github/workflows/linting.yml
+++ b/.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: |
diff --git a/.nf-core.yml b/.nf-core.yml
index dc7ee414..ea3d4a79 100644
--- a/.nf-core.yml
+++ b/.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
diff --git a/.prettierignore b/.prettierignore
index 2255e3e3..dd749d43 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/