Implement nf-test

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+
+.nf-test*

docs/output.md

@@ -321,7 +321,6 @@ Once installed, open IGV, go to `File > Open Session` and select the `igv_sessio
 - `genome/`
   - A number of genome-specific files are generated by the pipeline in order to aid in the filtering of the data, and because they are required by standard tools such as BEDTools. These can be found in this directory along with the genome fasta file which is required by IGV. If using a genome from AWS iGenomes and if it exists a `README.txt` file containing information about the annotation version will also be saved in this directory.
 - `genome/index/`
-
   - `bwa/`: Directory containing BWA indices.
   - `bowtie2/`: Directory containing BOWTIE2 indices.
   - `chromap/`: Directory containing Chromap indices.

modules/local/bam_remove_orphans.nf

@@ -43,4 +43,15 @@ process BAM_REMOVE_ORPHANS {
         END_VERSIONS
         """
     }
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/local/bamtools_filter.nf

@@ -40,4 +40,16 @@ process BAMTOOLS_FILTER {
         bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//')
+    END_VERSIONS
+    """
 }

modules/local/bedtools_genomecov.nf

@@ -40,4 +40,16 @@ process BEDTOOLS_GENOMECOV {
         bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bedGraph
+    touch ${prefix}.scale_factor.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
 }

modules/local/frip_score.nf

@@ -31,4 +31,16 @@ process FRIP_SCORE {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.FRiP.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/local/multiqc.nf

@@ -71,4 +71,16 @@ process MULTIQC {
         multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir -p multiqc_data
+    touch multiqc_report.html
+    touch multiqc_data/multiqc.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
 }

modules/local/multiqc_custom_phantompeakqualtools.nf

@@ -33,4 +33,17 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.spp_nsc_mqc.tsv
+    touch ${prefix}.spp_rsc_mqc.tsv
+    touch ${prefix}.spp_correlation_mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

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

@@ -0,0 +1,57 @@
+nextflow_pipeline {
+
+    name "Test pipeline with bowtie2 aligner"
+    script "../main.nf"
+    tag "bowtie2"
+
+    test("bowtie2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$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() }
+            )
+        }
+    }
+
+    test("bowtie2 with stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+}