test: Implement nft-utils for enhanced snapshot testing

- Update nft-utils plugin from v0.0.3 to v0.0.5
- Replace basic snapshot assertions with nft-utils functions:
  - Use removeNextflowVersion() to eliminate timestamp variations
  - Add getAllFilesFromDir() for comprehensive file structure snapshots
  - Exclude unstable execution files for consistent CI testing
- Enhance all test files: bowtie2, chromap, star, skip_trimming, skip_consensus_peaks
- Maintain correct test expectations (main tests fail, stub tests pass)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

nf-test.config

@@ -19,6 +19,6 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "[email protected].3"
+        load "[email protected].5"
     }
 }

tests/.nftignore

@@ -1,11 +1,84 @@
+# === SYSTEM FILES ===
 .DS_Store
+**/.DS_Store
+
+# === PIPELINE EXECUTION METADATA ===
+pipeline_info/*.{html,json,txt,yml}
+
+# === MULTIQC OUTPUTS ===
+# MultiQC files contain timestamps, system paths, and run-specific data
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
 multiqc/multiqc_data/BETA-multiqc.parquet
-multiqc/multiqc_data/multiqc.log
-multiqc/multiqc_data/multiqc_data.json
+**/multiqc.log
+**/multiqc_data.json
+**/multiqc_report.html
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
-multiqc/multiqc_report.html
+
+# === QC TOOL OUTPUTS ===
 fastqc/*_fastqc.{html,zip}
-pipeline_info/*.{html,json,txt,yml}
+**/*_fastqc.html
+**/*_val_*_fastqc.html
+
+# === BINARY AND COMPRESSED FILES ===
+**/*.{pdf,png,svg,gz,bam,bai,bigWig,zip,RData,rds}
+
+# === TOOL-SPECIFIC METRICS FILES ===
+# Picard metrics
+**/*.quality_distribution_metrics
+**/*.quality_by_cycle_metrics
+**/*.insert_size_metrics
+**/*.alignment_summary_metrics
+**/*.base_distribution_by_cycle_metrics
+**/*.MarkDuplicates.metrics.txt
+
+# Trimming reports
+**/*_trimming_report.txt
+
+# Generic outputs
+**/*.out
+
+# === ANALYSIS RESULTS (FLOATING-POINT VARIATIONS) ===
+# DeepTools outputs
+**/*.plotFingerprint.raw.txt
+**/*.plotFingerprint.qcmetrics.txt
+**/*.computeMatrix.vals.mat.tab
+**/*.plotHeatmap.mat.tab
+**/*.computeMatrix.mat.gz
+**/*.plotProfile.tab
+
+# Peak calling and annotation
+**/*.annotatePeaks.txt
+**/*.boolean.annotatePeaks.txt
+**/macs3_peak.summary.txt
+
+# Feature counting
+**/*.featureCounts.txt
+**/*.featureCounts.txt.summary
+
+# Statistical analysis
+**/*.pca.vals.txt
+**/*.pca.vals_mqc.tsv
+**/*.sample.dists.txt
+**/*.sample.dists_mqc.tsv
+
+# === YAML CONFIGURATION FILES ===
+**/deeptools_plot_profile_mlib_deeptools.yaml
+**/multiqc_deseq2_clustering_1.yaml
+**/multiqc_deseq2_pca_1.yaml
+**/multiqc_sources.yaml
+**/read_distribution_profile.yaml
+**/deeptools_fingerprint_plot.yaml
+**/deeptools_plot_fingerprint_counts_mlib_deeptools.yaml
+
+# === CHIP-SEQ SPECIFIC OUTPUTS ===
+# PhantomPeakQualTools outputs (contain variable correlation data)
+**/*.spp_correlation_mqc.tsv
+**/*.spp_nsc_mqc.tsv
+**/*.spp_rsc_mqc.tsv
+
+# === IGV SESSION FILES ===
+# IGV session files contain absolute paths and timestamps
+**/igv_files.txt
+**/igv_session.xml

tests/bowtie2.nf.test

@@ -14,12 +14,21 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
+                    // Number of successful tasks
                     workflow.trace.succeeded().size(),
-                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
-                    file("$outputDir/multiqc/multiqc_report.html").name
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
                 ).match() }
             )
         }

tests/bowtie2.nf.test.snap

@@ -14,12 +14,21 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
+                    // Number of successful tasks
                     workflow.trace.succeeded().size(),
-                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
-                    file("$outputDir/multiqc/multiqc_report.html").name
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
                 ).match() }
             )
         }