add nf-test for alevin aligner

.gitignore

@@ -9,3 +9,4 @@ testing*
 log/
 reports/
 testme.sh
+.nf-test/

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "docker"
+
+}

tests/main_pipeline_alevin.test

@@ -0,0 +1,68 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("test-dataset_alevin_aligner") {
+
+        when {
+            // the rest is taken from shared config
+            params {
+                aligner    = 'alevin'
+                outdir     = "${outputDir}/results_alevin"
+
+                // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+            }
+        }
+
+        then {
+
+            //
+            // General assertions
+            //
+
+                // Did it finish successfully?
+                assert workflow.success
+
+                // How many tasks were executed?
+                assert workflow.trace.tasks().size() == 16
+
+                // How many results were produced?
+                assert path("${outputDir}/results_alevin").list().size() == 5
+                assert path("${outputDir}/results_alevin/alevin").list().size() == 4
+                assert path("${outputDir}/results_alevin/alevin/mtx_conversions").list().size() == 4
+                assert path("${outputDir}/results_alevin/alevinqc").list().size() == 2
+                assert path("${outputDir}/results_alevin/fastqc").list().size() == 12
+                assert path("${outputDir}/results_alevin/multiqc").list().size() == 3
+
+            //
+            // Check if files were produced
+            //
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_cols.txt" ).exists()
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat.mtx" ).exists()
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_rows.txt" ).exists()
+
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_cols.txt" ).exists()
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat.mtx" ).exists()
+            assert new File( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_rows.txt" ).exists()
+
+            //
+            // Check if files are the same
+            //
+            assert snapshot(
+                workflow,
+                path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_cols.txt" ),
+                path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat.mtx" ),
+                path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_rows.txt" ),
+                path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_cols.txt" ),
+                path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat.mtx" ),
+                path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_rows.txt" )
+            ).match()
+
+        }
+    }
+
+}

tests/main_pipeline_alevin.test.snap

@@ -0,0 +1,32 @@
+{
+    "test-dataset_alevin_aligner": {
+        "content": [
+            {
+                "stderr": [
+
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 16,
+                    "tasksSucceeded": 16
+                },
+                "name": "workflow",
+                "success": true
+            },
+            "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97",
+            "quants_mat.mtx:md5,b8aa7b3c488fd8923de50a3621d4991f",
+            "quants_mat_rows.txt:md5,6227df5a13127b71c71fb18cd8574857",
+            "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97",
+            "quants_mat.mtx:md5,54cd12666016adce94c025b2e07f4b02",
+            "quants_mat_rows.txt:md5,6b458a7777260ba90eccbe7919df934b"
+        ],
+        "timestamp": "2024-01-19T10:28:35.652763852"
+    }
+}

tests/nextflow.config

@@ -0,0 +1,32 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+// Copy from test.config for standardization
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input        = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv'
+
+    // Genome references
+    fasta        = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa'
+    gtf          = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf'
+    protocol     = '10XV2'
+
+    validationSchemaIgnoreParams = 'genomes'
+}
+
+process {
+    withName: '.*:CELLRANGER_COUNT' {
+        maxForks = 1
+    }
+}