Add test suite for UMI handling functionality

CHANGELOG.md

@@ -17,6 +17,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1369](https://github.com/nf-core/rnaseq/pull/1369) - Add umicollapse as an alternative to umi-tools
 - [PR #1461](https://github.com/nf-core/rnaseq/pull/1461) - Add FASTQ linting during preprocessing
 - [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
+- [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
 
 ### Software dependencies
 

tests/.nftignore

@@ -13,6 +13,7 @@ star_rsem/*.{genes,isoforms}.results
 star_rsem/log/*.log
 star_salmon/log/*.Log.{final.out,out,progress.out}
 trimgalore/*fastq.gz_trimming_report.txt
+umitools/*.umi_extract.log
 {hisat2,star_rsem,star_salmon}/*.{bam,bam.bai}
 {hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig
 {hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf
@@ -31,6 +32,7 @@ trimgalore/*fastq.gz_trimming_report.txt
 {hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab
 {hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt
 {hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf
+{hisat2,star_rsem,star_salmon}/umitools/genomic_dedup_log/*_UMICollapse.log
 {multiqc,multiqc/**}/multiqc_report.html
 {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
 {multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt
@@ -81,6 +83,8 @@ trimgalore/*fastq.gz_trimming_report.txt
 {salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt
 {salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/*.txt
 {salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData
+{salmon,star_rsem,star_salmon}/umitools/{genomic,transcriptomic}_dedup_log/*
+{salmon,star_rsem,star_salmon}/umitools/prepare_for_salmon_log/*
 {salmon,star_salmon}/*/aux_info/fld.gz
 {salmon,star_salmon}/*/aux_info/meta_info.json
 {salmon,star_salmon}/*/libParams/flenDist.txt

tests/umi.nf.test

@@ -0,0 +1,110 @@
+nextflow_pipeline {
+
+    name "Test pipeline with dummy UMI settings"
+    script "../main.nf"
+
+    test("Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'") {
+
+        when {
+            params {
+                with_umi = true
+                umitools_extract_method = "regex"
+                umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*"
+                umitools_dedup_stats = true
+                skip_bbsplit = true
+                umi_dedup_tool = 'umicollapse'
+                aligner = 'hisat2'
+                outdir = "$outputDir"
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("--umi_dedup_tool 'umitools'") {
+
+        when {
+            params {
+                with_umi = true
+                umitools_extract_method = "regex"
+                umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*"
+                umitools_dedup_stats = true
+                skip_bbsplit = true
+                outdir = "$outputDir"
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("--umi_dedup_tool 'umitools - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                with_umi = true
+                umitools_extract_method = "regex"
+                umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*"
+                umitools_dedup_stats = true
+                outdir = "$outputDir"
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}