test: disable MultiQC plot export in test profile for deterministic snapshots

MultiQC only renders multiqc_plots/ where its kaleido backend works (linux/amd64)
and silently skips it on other archs (e.g. arm64, or amd64 under Rosetta), which
made the default test's file-list snapshot environment-dependent. Instead of
excluding the plots from the assertion, disable export_plots for tests via a new
assets/multiqc_test_config.yml wired through the test profile's multiqc_config.
Production runs keep export_plots: true.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: znorgaard

assets/multiqc_test_config.yml

@@ -0,0 +1,6 @@
+# Test-only MultiQC overrides, merged on top of assets/multiqc_config.yml.
+# Disable static plot export (multiqc_plots/) so the test output is deterministic across
+# architectures: MultiQC only renders multiqc_plots/ where its kaleido backend works
+# (linux/amd64) and skips it elsewhere (e.g. arm64, or amd64 under Rosetta), which made the
+# file-list snapshot environment-dependent. Production runs keep export_plots: true.
+export_plots: false

conf/test.config

@@ -23,6 +23,10 @@ params {
 
     // Genome references
     fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/references/chr17.fa"
+
+    // Disable MultiQC static plot export so the output file list is deterministic across
+    // architectures (multiqc_plots/ is only rendered where kaleido works, e.g. linux/amd64).
+    multiqc_config = "${projectDir}/assets/multiqc_test_config.yml"
 }
 
 validation {

docs/CONTRIBUTING.md

@@ -77,6 +77,14 @@ Update the snapshots with the following command:
 nf-test test --tag test --profile +docker --verbose --update-snapshots
 ```
 
+> [!NOTE]
+> The `test` profile sets `multiqc_config = assets/multiqc_test_config.yml`, which disables
+> MultiQC static plot export (`export_plots: false`). MultiQC only renders `multiqc/multiqc_plots/`
+> where its kaleido backend works (linux/amd64) and silently skips it elsewhere (e.g. arm64, or
+> amd64 under Rosetta), so leaving it enabled makes the file-list snapshot architecture-dependent.
+> Disabling it for tests keeps snapshots deterministic and reproducible on any architecture.
+> Production runs are unaffected — `assets/multiqc_config.yml` keeps `export_plots: true`.
+
 When you create a pull request with changes, GitHub Actions will run automatic tests.
 Pull requests are typically reviewed when these tests are passing.
 

tests/default.nf.test

@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            // multiqc_plots/ exports are environment-dependent (rendered on linux/amd64 CI but not on
-            // some local arch), so exclude them from the file-list snapshot for stability.
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'multiqc/multiqc_plots', 'multiqc/multiqc_plots/**'])
+            // (the test profile disables MultiQC static plot export, so multiqc_plots/ — which is
+            // only rendered on some architectures — never appears here and the list is deterministic)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             // bam_files: All bam files