From 739fbb55578267c3260e307bb3b29a7fedd5822e Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Fri, 19 Jan 2024 11:40:02 +0000
Subject: [PATCH 01/13] add nf-test for alevin aligner

---
 .gitignore                           |  1 +
 nf-test.config                       |  8 ++++
 tests/main_pipeline_alevin.test      | 68 ++++++++++++++++++++++++++++
 tests/main_pipeline_alevin.test.snap | 32 +++++++++++++
 tests/nextflow.config                | 32 +++++++++++++
 5 files changed, 141 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/main_pipeline_alevin.test
 create mode 100644 tests/main_pipeline_alevin.test.snap
 create mode 100644 tests/nextflow.config

diff --git a/.gitignore b/.gitignore
index 5d402163..a9ba2c52 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@ testing*
 log/
 reports/
 testme.sh
+.nf-test/
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..2fa82adf
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "docker"
+
+}
diff --git a/tests/main_pipeline_alevin.test b/tests/main_pipeline_alevin.test
new file mode 100644
index 00000000..c51a8ee9
--- /dev/null
+++ b/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()
+
+        }
+    }
+
+}
diff --git a/tests/main_pipeline_alevin.test.snap b/tests/main_pipeline_alevin.test.snap
new file mode 100644
index 00000000..9d194012
--- /dev/null
+++ b/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"
+    }
+}
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..66e56d29
--- /dev/null
+++ b/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
+    }
+}

From 23072dc4271f7b4461426fbe0a226d3e190d2b4a Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Fri, 19 Jan 2024 15:51:42 +0000
Subject: [PATCH 02/13] adding nf-test for star aligner

---
 tests/main_pipeline_star.test      | 87 ++++++++++++++++++++++++++++++
 tests/main_pipeline_star.test.snap | 38 +++++++++++++
 2 files changed, 125 insertions(+)
 create mode 100644 tests/main_pipeline_star.test
 create mode 100644 tests/main_pipeline_star.test.snap

diff --git a/tests/main_pipeline_star.test b/tests/main_pipeline_star.test
new file mode 100644
index 00000000..d20657f1
--- /dev/null
+++ b/tests/main_pipeline_star.test
@@ -0,0 +1,87 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("test-dataset_star_aligner") {
+
+        when {
+            // the rest is taken from shared config
+            params {
+                aligner    = 'star'
+                outdir     = "${outputDir}/results_star"
+
+                // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+            }
+        }
+
+        then {
+
+            //
+            // General assertions
+            //
+
+                // Did it finish successfully?
+                assert workflow.success
+
+                // How many tasks were executed?
+                assert workflow.trace.tasks().size() == 14
+
+                // How many results were produced?
+                assert path("${outputDir}/results_star").list().size() == 4
+                assert path("${outputDir}/results_star/star").list().size() == 3
+                assert path("${outputDir}/results_star/star/mtx_conversions").list().size() == 4
+                assert path("${outputDir}/results_star/fastqc").list().size() == 12
+                assert path("${outputDir}/results_star/multiqc").list().size() == 3
+
+            //
+            // Check if files were produced
+            //
+            //
+            // Check if main files exist
+            //
+
+            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
+            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.rds"  ).exists()
+
+            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.SJ.out.tab"                             ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Barcodes.stats"                ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/matrix.mtx.gz"   ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
+            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.rds"  ).exists()
+
+            //
+            // Check if files are the same
+            //
+            assert snapshot(
+                workflow,
+                path( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ),
+                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ),
+                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
+                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/features.tsv.gz" ),
+                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
+                // path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ), // does not match
+                path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.rds"  ),
+                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.SJ.out.tab"                             ),
+                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Barcodes.stats"                ),
+                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
+                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/features.tsv.gz" ),
+                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
+                // path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ), // does not match
+                path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.rds"  ),
+            ).match()
+
+        }
+    }
+
+}
diff --git a/tests/main_pipeline_star.test.snap b/tests/main_pipeline_star.test.snap
new file mode 100644
index 00000000..ef086f60
--- /dev/null
+++ b/tests/main_pipeline_star.test.snap
@@ -0,0 +1,38 @@
+{
+    "test-dataset_star_aligner": {
+        "content": [
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+                    
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 14,
+                    "tasksSucceeded": 14
+                },
+                "name": "workflow",
+                "success": true
+            },
+            "Sample_X.SJ.out.tab:md5,d2d7f0abe38029012571bdf6622fc6eb",
+            "Barcodes.stats:md5,7f99dc8aa5e074fbe5779ea7712c0886",
+            "matrix.mtx.gz:md5,6a923393343aa1a69b0cf1bd998c9285",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "barcodes.tsv.gz:md5,9a7dacaa1779ea43c1507a947fe6992a",
+            "Sample_X_matrix.rds:md5,aa2d36dd8507aba864347c88e4ce0d27",
+            "Sample_Y.SJ.out.tab:md5,98bd31104a860cf80119dc30d938d163",
+            "Barcodes.stats:md5,2dbf1ae426c1afd97903ee001f0db5ce",
+            "matrix.mtx.gz:md5,0ae080bd0002e350531a5816e159345e",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "barcodes.tsv.gz:md5,9b695b0b91bcb146ec9c4688ca10a690",
+            "Sample_Y_matrix.rds:md5,d459af8f99258bcc88b80b2f7c58e911"
+        ],
+        "timestamp": "2024-01-19T15:46:22.470527538"
+    }
+}
\ No newline at end of file

From 4ae28e384a4e28fa2e4e5bc8bfe3536c4b1d407a Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 23 Jan 2024 11:51:02 +0000
Subject: [PATCH 03/13] add nf-tests for cellranger aligner

---
 tests/main_pipeline_cellranger.test      | 84 ++++++++++++++++++++++++
 tests/main_pipeline_cellranger.test.snap | 40 +++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 tests/main_pipeline_cellranger.test
 create mode 100644 tests/main_pipeline_cellranger.test.snap

diff --git a/tests/main_pipeline_cellranger.test b/tests/main_pipeline_cellranger.test
new file mode 100644
index 00000000..c90436f6
--- /dev/null
+++ b/tests/main_pipeline_cellranger.test
@@ -0,0 +1,84 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("test-dataset_cellranger_aligner") {
+
+        when {
+            // the rest is taken from shared config
+            params {
+                aligner    = 'cellranger'
+                outdir     = "${outputDir}/results_cellranger"
+
+                // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+            }
+        }
+
+        then {
+
+            //
+            // General assertions
+            //
+
+                // Did it finish successfully?
+                assert workflow.success
+
+                // How many tasks were executed?
+                assert workflow.trace.tasks().size() == 15
+
+                // How many results were produced?
+                assert path("${outputDir}/results_cellranger").list().size() == 4
+                assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4
+                assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4
+                assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3
+                assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12
+                assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3
+
+            //
+            // Check if files were produced
+            //
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz"   ).exists()
+
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz"   ).exists()
+
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz"   ).exists()
+
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz"   ).exists()
+
+            //
+            // Check if files are the same
+            //
+            assert snapshot(
+                workflow,
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
+                path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+            ).match()
+
+        }
+    }
+
+}
diff --git a/tests/main_pipeline_cellranger.test.snap b/tests/main_pipeline_cellranger.test.snap
new file mode 100644
index 00000000..5f88b954
--- /dev/null
+++ b/tests/main_pipeline_cellranger.test.snap
@@ -0,0 +1,40 @@
+{
+    "test-dataset_cellranger_aligner": {
+        "content": [
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+                    
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 15,
+                    "tasksSucceeded": 15
+                },
+                "name": "workflow",
+                "success": true
+            },
+            "barcodes.tsv.gz:md5,fe6e51564b4405b37ca8604a844b1f2e",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "matrix.mtx.gz:md5,79471f700ec5bab852a960f0d1537705",
+            "barcodes.tsv.gz:md5,77afe9a76631fc7b44236d3962a55aa5",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "matrix.mtx.gz:md5,e224aa759250fa5730dc069bce9be253",
+            "barcodes.tsv.gz:md5,85da6b6e0c78dfe81af8c07c2017ab5e",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "matrix.mtx.gz:md5,1bc71041a425bfcee38472bfec5997f8",
+            "barcodes.tsv.gz:md5,081f72b5252ccaf5ffd535ffbd235c4c",
+            "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+            "matrix.mtx.gz:md5,a4db04e43e650accc96361a287126a6b",
+            "Sample_X_matrix.rds:md5,f9191ba575a3ab79ada4807715f18573",
+            "Sample_Y_matrix.rds:md5,7be3f7b29d668dcf7e951b9f4d371a5e"
+        ],
+        "timestamp": "2024-01-22T15:19:20.134275449"
+    }
+}
\ No newline at end of file

From b56577ce413a2a93ecc950b85bd1a7e0e235e38f Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 23 Jan 2024 12:25:46 +0000
Subject: [PATCH 04/13] add nf-test for kallisto aligner

---
 tests/main_pipeline_kallisto.test      | 71 ++++++++++++++++++++++++++
 tests/main_pipeline_kallisto.test.snap | 34 ++++++++++++
 2 files changed, 105 insertions(+)
 create mode 100644 tests/main_pipeline_kallisto.test
 create mode 100644 tests/main_pipeline_kallisto.test.snap

diff --git a/tests/main_pipeline_kallisto.test b/tests/main_pipeline_kallisto.test
new file mode 100644
index 00000000..3bae1f31
--- /dev/null
+++ b/tests/main_pipeline_kallisto.test
@@ -0,0 +1,71 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("test-dataset_kallisto_aligner") {
+
+        when {
+            // the rest is taken from shared config
+            params {
+                aligner    = 'kallisto'
+                outdir     = "${outputDir}/results_kallisto"
+
+                // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+            }
+        }
+
+        then {
+
+            //
+            // General assertions
+            //
+
+                // Did it finish successfully?
+                assert workflow.success
+
+                // How many tasks were executed?
+                assert workflow.trace.tasks().size() == 14
+
+                // How many results were produced?
+                assert path("${outputDir}/results_kallisto").list().size() == 4
+                assert path("${outputDir}/results_kallisto/kallisto").list().size() == 4
+                assert path("${outputDir}/results_kallisto/kallisto/mtx_conversions").list().size() == 4
+                assert path("${outputDir}/results_kallisto/kallisto/Sample_X.count").list().size() == 9
+                assert path("${outputDir}/results_kallisto/kallisto/Sample_Y.count").list().size() == 9
+                assert path("${outputDir}/results_kallisto/fastqc").list().size() == 12
+                assert path("${outputDir}/results_kallisto/multiqc").list().size() == 3
+
+            //
+            // Check if files were produced
+            //
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt"    ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx"          ).exists()
+
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.barcodes.txt" ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.genes.txt"    ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.mtx"          ).exists()
+
+            //
+            // Check if files are the same
+            //
+            assert snapshot(
+                workflow,
+                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
+                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt" ),
+                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx" ),
+                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
+                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.genes.txt" ),
+                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.mtx" ),
+                path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
+                path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+            ).match()
+
+        }
+    }
+
+}
diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.test.snap
new file mode 100644
index 00000000..b0fb50bb
--- /dev/null
+++ b/tests/main_pipeline_kallisto.test.snap
@@ -0,0 +1,34 @@
+{
+    "test-dataset_kallisto_aligner": {
+        "content": [
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+                    
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 14,
+                    "tasksSucceeded": 14
+                },
+                "name": "workflow",
+                "success": true
+            },
+            "cells_x_genes.barcodes.txt:md5,18be561873e435d4587f6b3f95a0e301",
+            "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
+            "cells_x_genes.mtx:md5,37d2cd8c712f9c70463e87485bf6cd36",
+            "cells_x_genes.barcodes.txt:md5,488437e1f5477243697efb93366e5676",
+            "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
+            "cells_x_genes.mtx:md5,af90e05b404490f6cb133ab7f62949f8",
+            "Sample_X_matrix.rds:md5,f0e43f69403f4b2e7704065421592ad0",
+            "Sample_Y_matrix.rds:md5,61809156e64dbdaf254cbc1c3456588e"
+        ],
+        "timestamp": "2024-01-23T12:19:47.921508953"
+    }
+}
\ No newline at end of file

From 3a89373a5594d674e807e7936fb72ab76ecdb2ab Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:01:17 +0000
Subject: [PATCH 05/13] update tests

---
 tests/main_pipeline_alevin.test     | 31 ++++++++++-------------
 tests/main_pipeline_cellranger.test | 39 ++++++++++-------------------
 tests/main_pipeline_kallisto.test   | 33 +++++++++++-------------
 tests/main_pipeline_star.test       | 37 ++++++++-------------------
 4 files changed, 50 insertions(+), 90 deletions(-)

diff --git a/tests/main_pipeline_alevin.test b/tests/main_pipeline_alevin.test
index c51a8ee9..f2730699 100644
--- a/tests/main_pipeline_alevin.test
+++ b/tests/main_pipeline_alevin.test
@@ -24,30 +24,25 @@ nextflow_pipeline {
             // General assertions
             //
 
-                // Did it finish successfully?
-                assert workflow.success
+            // Did it finish successfully?
+            assert workflow.success
 
-                // How many tasks were executed?
-                assert workflow.trace.tasks().size() == 16
+            // 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
+            // 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()
+            assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
+            assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
 
             //
             // Check if files are the same
diff --git a/tests/main_pipeline_cellranger.test b/tests/main_pipeline_cellranger.test
index c90436f6..314177e0 100644
--- a/tests/main_pipeline_cellranger.test
+++ b/tests/main_pipeline_cellranger.test
@@ -24,38 +24,25 @@ nextflow_pipeline {
             // General assertions
             //
 
-                // Did it finish successfully?
-                assert workflow.success
+            // Did it finish successfully?
+            assert workflow.success
 
-                // How many tasks were executed?
-                assert workflow.trace.tasks().size() == 15
+            // How many tasks were executed?
+            assert workflow.trace.tasks().size() == 15
 
-                // How many results were produced?
-                assert path("${outputDir}/results_cellranger").list().size() == 4
-                assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4
-                assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4
-                assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3
-                assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12
-                assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3
+            // How many results were produced?
+            assert path("${outputDir}/results_cellranger").list().size() == 4
+            assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4
+            assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4
+            assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3
+            assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12
+            assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3
 
             //
             // Check if files were produced
             //
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz"   ).exists()
-
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz"   ).exists()
-
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz"   ).exists()
-
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz"   ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
+            assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
 
             //
             // Check if files are the same
diff --git a/tests/main_pipeline_kallisto.test b/tests/main_pipeline_kallisto.test
index 3bae1f31..1b06f249 100644
--- a/tests/main_pipeline_kallisto.test
+++ b/tests/main_pipeline_kallisto.test
@@ -24,31 +24,26 @@ nextflow_pipeline {
             // General assertions
             //
 
-                // Did it finish successfully?
-                assert workflow.success
+            // Did it finish successfully?
+            assert workflow.success
 
-                // How many tasks were executed?
-                assert workflow.trace.tasks().size() == 14
+            // How many tasks were executed?
+            assert workflow.trace.tasks().size() == 14
 
-                // How many results were produced?
-                assert path("${outputDir}/results_kallisto").list().size() == 4
-                assert path("${outputDir}/results_kallisto/kallisto").list().size() == 4
-                assert path("${outputDir}/results_kallisto/kallisto/mtx_conversions").list().size() == 4
-                assert path("${outputDir}/results_kallisto/kallisto/Sample_X.count").list().size() == 9
-                assert path("${outputDir}/results_kallisto/kallisto/Sample_Y.count").list().size() == 9
-                assert path("${outputDir}/results_kallisto/fastqc").list().size() == 12
-                assert path("${outputDir}/results_kallisto/multiqc").list().size() == 3
+            // How many results were produced?
+            assert path("${outputDir}/results_kallisto").list().size() == 4
+            assert path("${outputDir}/results_kallisto/kallisto").list().size() == 4
+            assert path("${outputDir}/results_kallisto/kallisto/mtx_conversions").list().size() == 4
+            assert path("${outputDir}/results_kallisto/kallisto/Sample_X.count").list().size() == 9
+            assert path("${outputDir}/results_kallisto/kallisto/Sample_Y.count").list().size() == 9
+            assert path("${outputDir}/results_kallisto/fastqc").list().size() == 12
+            assert path("${outputDir}/results_kallisto/multiqc").list().size() == 3
 
             //
             // Check if files were produced
             //
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ).exists()
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt"    ).exists()
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx"          ).exists()
-
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.barcodes.txt" ).exists()
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.genes.txt"    ).exists()
-            assert new File( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.mtx"          ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
+            assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
 
             //
             // Check if files are the same
diff --git a/tests/main_pipeline_star.test b/tests/main_pipeline_star.test
index d20657f1..de07c8d3 100644
--- a/tests/main_pipeline_star.test
+++ b/tests/main_pipeline_star.test
@@ -24,41 +24,24 @@ nextflow_pipeline {
             // General assertions
             //
 
-                // Did it finish successfully?
-                assert workflow.success
+            // Did it finish successfully?
+            assert workflow.success
 
-                // How many tasks were executed?
-                assert workflow.trace.tasks().size() == 14
+            // How many tasks were executed?
+            assert workflow.trace.tasks().size() == 14
 
-                // How many results were produced?
-                assert path("${outputDir}/results_star").list().size() == 4
-                assert path("${outputDir}/results_star/star").list().size() == 3
-                assert path("${outputDir}/results_star/star/mtx_conversions").list().size() == 4
-                assert path("${outputDir}/results_star/fastqc").list().size() == 12
-                assert path("${outputDir}/results_star/multiqc").list().size() == 3
+            // How many results were produced?
+            assert path("${outputDir}/results_star").list().size() == 4
+            assert path("${outputDir}/results_star/star").list().size() == 3
+            assert path("${outputDir}/results_star/star/mtx_conversions").list().size() == 4
+            assert path("${outputDir}/results_star/fastqc").list().size() == 12
+            assert path("${outputDir}/results_star/multiqc").list().size() == 3
 
             //
             // Check if files were produced
             //
-            //
-            // Check if main files exist
-            //
-
-            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/barcodes.tsv.gz" ).exists()
             assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.rds"  ).exists()
-
-            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.SJ.out.tab"                             ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Barcodes.stats"                ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/matrix.mtx.gz"   ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/features.tsv.gz" ).exists()
-            assert new File( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/barcodes.tsv.gz" ).exists()
             assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.rds"  ).exists()
 
             //
             // Check if files are the same

From ce0db16615336546d6683f5ec4da36b0b2316edb Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:15:15 +0000
Subject: [PATCH 06/13] update ci.yml for nf-test

---
 .github/workflows/ci.yml | 68 +++++++++++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e8907caf..574c5fd3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,39 +1,43 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.1"
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
+    name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    needs: [changes, define_nxf_versions]
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        profile: [
-            "test,docker --aligner alevin",
-            "test,docker --aligner kallisto",
-            "test,docker --aligner star",
-            "test,docker --aligner cellranger",
-            # "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
-            # "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
+        profile:
+          [
+            "tests/main_pipeline_alevin.test",
+            "tests/main_pipeline_cellranger.test",
+            "tests/main_pipeline_kallisto.test",
+            "tests/main_pipeline_star.test",
           ]
+
     steps:
       - name: Free some space
         run: |
@@ -41,6 +45,7 @@ jobs:
           sudo rm -rf /opt/ghc
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
       - name: Check out pipeline code
         uses: actions/checkout@v4
 
@@ -49,8 +54,33 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} --outdir ./results
+          nf-test test "${{ matrix.profile }}" --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

From 4df4fbfce20b91b868518b267e2dce9d68e78f35 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:16:37 +0000
Subject: [PATCH 07/13] also allow on push

---
 .github/workflows/ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 574c5fd3..ddecad72 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,9 @@
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 name: nf-core CI
 on:
+  push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]

From ae786d60635bf082c5d3fd4fa3c6326167e03460 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:18:20 +0000
Subject: [PATCH 08/13] add if and remove needs

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ddecad72..8413df7e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ concurrency:
 jobs:
   test:
     name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
-    needs: [changes, define_nxf_versions]
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false

From e806454af392db3bd518c506c21674ebc2202ec7 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:20:40 +0000
Subject: [PATCH 09/13] modify names to have only aligner name

---
 .github/workflows/ci.yml | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8413df7e..16953daa 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ concurrency:
 
 jobs:
   test:
-    name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
     runs-on: ubuntu-latest
     strategy:
@@ -33,13 +33,7 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        profile:
-          [
-            "tests/main_pipeline_alevin.test",
-            "tests/main_pipeline_cellranger.test",
-            "tests/main_pipeline_kallisto.test",
-            "tests/main_pipeline_star.test",
-          ]
+        profile: ["alevin", "cellranger", "kallisto", "star"]
 
     steps:
       - name: Free some space
@@ -74,7 +68,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test "${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test tests/main_pipeline_"${{ matrix.profile }}".test --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

From a2aeea40f2688c2b516ef2f49adc8f1505388c74 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 12:02:35 +0000
Subject: [PATCH 10/13] fix quotation

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 16953daa..ea9587e5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -68,7 +68,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test tests/main_pipeline_"${{ matrix.profile }}".test --junitxml=test.xml
+          "nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml"
 
       - name: Output log on failure
         if: failure()

From 8684445e6d2233b2117cfcd7894b862388312323 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 12:03:50 +0000
Subject: [PATCH 11/13] removing quotations

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ea9587e5..36d997da 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -68,7 +68,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          "nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml"
+          nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

From da1eadeab233fc4500dcc5ebb2d34b7f9b9d7966 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Wed, 14 Feb 2024 08:15:48 +0000
Subject: [PATCH 12/13] updated tests to use assertAll()

---
 tests/main_pipeline_alevin.test     | 76 +++++++++++++-------------
 tests/main_pipeline_cellranger.test | 82 +++++++++++++++--------------
 tests/main_pipeline_kallisto.test   | 72 +++++++++++++------------
 tests/main_pipeline_star.test       | 80 +++++++++++++++-------------
 4 files changed, 163 insertions(+), 147 deletions(-)

diff --git a/tests/main_pipeline_alevin.test b/tests/main_pipeline_alevin.test
index f2730699..303a625b 100644
--- a/tests/main_pipeline_alevin.test
+++ b/tests/main_pipeline_alevin.test
@@ -20,42 +20,46 @@ nextflow_pipeline {
 
         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( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).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()
+            assertAll(
+
+                //
+                // 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( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).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()}
+
+            ) // end of assertAll()
 
         }
     }
diff --git a/tests/main_pipeline_cellranger.test b/tests/main_pipeline_cellranger.test
index 314177e0..996c0f76 100644
--- a/tests/main_pipeline_cellranger.test
+++ b/tests/main_pipeline_cellranger.test
@@ -20,50 +20,54 @@ nextflow_pipeline {
 
         then {
 
-            //
-            // General assertions
-            //
+            assertAll(
 
-            // Did it finish successfully?
-            assert workflow.success
+                //
+                // General assertions
+                //
 
-            // How many tasks were executed?
-            assert workflow.trace.tasks().size() == 15
+                // Did it finish successfully?
+                {assert workflow.success},
 
-            // How many results were produced?
-            assert path("${outputDir}/results_cellranger").list().size() == 4
-            assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4
-            assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4
-            assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3
-            assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12
-            assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3
+                // How many tasks were executed?
+                {assert workflow.trace.tasks().size() == 15},
 
-            //
-            // Check if files were produced
-            //
-            assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
+                // How many results were produced?
+                {assert path("${outputDir}/results_cellranger").list().size() == 4},
+                {assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4},
+                {assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4},
+                {assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3},
+                {assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12},
+                {assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3},
 
-            //
-            // Check if files are the same
-            //
-            assert snapshot(
-                workflow,
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
-                path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
-                path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
-            ).match()
+                //
+                // Check if files were produced
+                //
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+
+                //
+                // Check if files are the same
+                //
+                {assert snapshot(
+                    workflow,
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+                ).match()}
+
+            ) // end of assertAll()
 
         }
     }
diff --git a/tests/main_pipeline_kallisto.test b/tests/main_pipeline_kallisto.test
index 1b06f249..98ede8c4 100644
--- a/tests/main_pipeline_kallisto.test
+++ b/tests/main_pipeline_kallisto.test
@@ -20,45 +20,49 @@ nextflow_pipeline {
 
         then {
 
-            //
-            // General assertions
-            //
+            assertAll(
 
-            // Did it finish successfully?
-            assert workflow.success
+                //
+                // General assertions
+                //
 
-            // How many tasks were executed?
-            assert workflow.trace.tasks().size() == 14
+                // Did it finish successfully?
+                {assert workflow.success},
 
-            // How many results were produced?
-            assert path("${outputDir}/results_kallisto").list().size() == 4
-            assert path("${outputDir}/results_kallisto/kallisto").list().size() == 4
-            assert path("${outputDir}/results_kallisto/kallisto/mtx_conversions").list().size() == 4
-            assert path("${outputDir}/results_kallisto/kallisto/Sample_X.count").list().size() == 9
-            assert path("${outputDir}/results_kallisto/kallisto/Sample_Y.count").list().size() == 9
-            assert path("${outputDir}/results_kallisto/fastqc").list().size() == 12
-            assert path("${outputDir}/results_kallisto/multiqc").list().size() == 3
+                // How many tasks were executed?
+                {assert workflow.trace.tasks().size() == 14},
 
-            //
-            // Check if files were produced
-            //
-            assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
+                // How many results were produced?
+                {assert path("${outputDir}/results_kallisto").list().size() == 4},
+                {assert path("${outputDir}/results_kallisto/kallisto").list().size() == 4},
+                {assert path("${outputDir}/results_kallisto/kallisto/mtx_conversions").list().size() == 4},
+                {assert path("${outputDir}/results_kallisto/kallisto/Sample_X.count").list().size() == 9},
+                {assert path("${outputDir}/results_kallisto/kallisto/Sample_Y.count").list().size() == 9},
+                {assert path("${outputDir}/results_kallisto/fastqc").list().size() == 12},
+                {assert path("${outputDir}/results_kallisto/multiqc").list().size() == 3},
 
-            //
-            // Check if files are the same
-            //
-            assert snapshot(
-                workflow,
-                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
-                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt" ),
-                path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx" ),
-                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
-                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.genes.txt" ),
-                path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.mtx" ),
-                path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
-                path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
-            ).match()
+                //
+                // Check if files were produced
+                //
+                {assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+
+                //
+                // Check if files are the same
+                //
+                {assert snapshot(
+                    workflow,
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt" ),
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx" ),
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.genes.txt" ),
+                    path( "${outputDir}/results_kallisto/kallisto/Sample_Y.count/counts_unfiltered/cells_x_genes.mtx" ),
+                    path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
+                    path( "${outputDir}/results_kallisto/kallisto/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+                ).match()}
+
+            ) // end of assertAll()
 
         }
     }
diff --git a/tests/main_pipeline_star.test b/tests/main_pipeline_star.test
index de07c8d3..6616ea87 100644
--- a/tests/main_pipeline_star.test
+++ b/tests/main_pipeline_star.test
@@ -20,49 +20,53 @@ nextflow_pipeline {
 
         then {
 
-            //
-            // General assertions
-            //
+            assertAll(
 
-            // Did it finish successfully?
-            assert workflow.success
+                //
+                // General assertions
+                //
 
-            // How many tasks were executed?
-            assert workflow.trace.tasks().size() == 14
+                // Did it finish successfully?
+                {assert workflow.success},
 
-            // How many results were produced?
-            assert path("${outputDir}/results_star").list().size() == 4
-            assert path("${outputDir}/results_star/star").list().size() == 3
-            assert path("${outputDir}/results_star/star/mtx_conversions").list().size() == 4
-            assert path("${outputDir}/results_star/fastqc").list().size() == 12
-            assert path("${outputDir}/results_star/multiqc").list().size() == 3
+                // How many tasks were executed?
+                {assert workflow.trace.tasks().size() == 14},
 
-            //
-            // Check if files were produced
-            //
-            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()
-            assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()
+                // How many results were produced?
+                {assert path("${outputDir}/results_star").list().size() == 4},
+                {assert path("${outputDir}/results_star/star").list().size() == 3},
+                {assert path("${outputDir}/results_star/star/mtx_conversions").list().size() == 4},
+                {assert path("${outputDir}/results_star/fastqc").list().size() == 12},
+                {assert path("${outputDir}/results_star/multiqc").list().size() == 3},
 
-            //
-            // Check if files are the same
-            //
-            assert snapshot(
-                workflow,
-                path( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ),
-                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ),
-                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
-                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/features.tsv.gz" ),
-                path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
-                // path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ), // does not match
-                path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.rds"  ),
-                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.SJ.out.tab"                             ),
-                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Barcodes.stats"                ),
-                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
-                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/features.tsv.gz" ),
-                path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
-                // path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ), // does not match
-                path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.rds"  ),
-            ).match()
+                //
+                // Check if files were produced
+                //
+                {assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+
+                //
+                // Check if files are the same
+                //
+                {assert snapshot(
+                    workflow,
+                    path( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ),
+                    path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ),
+                    path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
+                    path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/features.tsv.gz" ),
+                    path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
+                    // path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ), // does not match
+                    path( "${outputDir}/results_star/star/mtx_conversions/Sample_X/Sample_X_matrix.rds"  ),
+                    path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.SJ.out.tab"                             ),
+                    path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Barcodes.stats"                ),
+                    path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/matrix.mtx.gz"   ),
+                    path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/features.tsv.gz" ),
+                    path( "${outputDir}/results_star/star/Sample_Y/Sample_Y.Solo.out/Gene/filtered/barcodes.tsv.gz" ),
+                    // path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ), // does not match
+                    path( "${outputDir}/results_star/star/mtx_conversions/Sample_Y/Sample_Y_matrix.rds"  ),
+                ).match()}
+
+            ) // end of assertAll()
 
         }
     }

From 0e5e6aabd05a2c0a12601f517f5eddb6ec56680b Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Wed, 14 Feb 2024 08:21:57 +0000
Subject: [PATCH 13/13] update changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a7c8ed27..9f920a4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## TBD
+
+- [[#91](https://github.com/nf-core/scrnaseq/issues/91)] - Change from pytests to nf-test
+
 ## v2.5.1
 
 - Fix that cellranger workflow couldn't be run and enable CI for this workflow ([#288](https://github.com/nf-core/scrnaseq/pull/288)).