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 <noreply@anthropic.com>

Author: edmundmiller

nf-test.config

@@ -19,6 +19,6 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-utils@0.0.3"
+        load "nft-utils@0.0.5"
     }
 }

tests/bowtie2.nf.test

@@ -20,8 +20,9 @@ nextflow_pipeline {
                 { assert workflow.failed },
                 { assert snapshot(
                     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
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    file("$outputDir/multiqc/multiqc_report.html").name,
+                    getAllFilesFromDir("$outputDir", false, ['pipeline_info/execution_*.{html,txt}'], null, ['*.html', '*.txt', '*.yml'])
                 ).match() }
             )
         }

tests/chromap.nf.test

@@ -20,8 +20,9 @@ nextflow_pipeline {
                 { assert workflow.failed },
                 { assert snapshot(
                     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
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    file("$outputDir/multiqc/multiqc_report.html").name,
+                    getAllFilesFromDir("$outputDir", false, ['pipeline_info/execution_*.{html,txt}'], null, ['*.html', '*.txt', '*.yml'])
                 ).match() }
             )
         }

tests/skip_consensus_peaks.nf.test

@@ -20,8 +20,9 @@ nextflow_pipeline {
                 { assert workflow.failed },
                 { assert snapshot(
                     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
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    file("$outputDir/multiqc/multiqc_report.html").name,
+                    getAllFilesFromDir("$outputDir", false, ['pipeline_info/execution_*.{html,txt}'], null, ['*.html', '*.txt', '*.yml'])
                 ).match() }
             )
         }

tests/skip_trimming.nf.test

@@ -20,8 +20,9 @@ nextflow_pipeline {
                 { assert workflow.failed },
                 { assert snapshot(
                     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
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    file("$outputDir/multiqc/multiqc_report.html").name,
+                    getAllFilesFromDir("$outputDir", false, ['pipeline_info/execution_*.{html,txt}'], null, ['*.html', '*.txt', '*.yml'])
                 ).match() }
             )
         }

tests/star.nf.test

@@ -20,8 +20,9 @@ nextflow_pipeline {
                 { assert workflow.failed },
                 { assert snapshot(
                     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
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
+                    file("$outputDir/multiqc/multiqc_report.html").name,
+                    getAllFilesFromDir("$outputDir", false, ['pipeline_info/execution_*.{html,txt}'], null, ['*.html', '*.txt', '*.yml'])
                 ).match() }
             )
         }