Convert bclconvert and bcl2fastq modules to nf-test (nf-core#4229)

* Convert bcl2fastq to nf-test

* Convert bclconvert tests to nf-test

* Sort snapshot to get a consistent file ordering

modules/nf-core/bcl2fastq/tests/main.nf.test

@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process BCL2FASTQ"
+    script "modules/nf-core/bcl2fastq/main.nf"
+    process "BCL2FASTQ"
+    config "./nextflow.config"
+    tag "bcl2fastq"
+    tag "modules"
+    tag "modules_nfcore"
+
+    test("homo sapiens illumina [bcl]") {
+        when {
+            process {
+                //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996
+                """
+                input[0] = [
+                    [ id: 'test', lane:1 ],
+                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/bcl2fastq/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args = "--tiles s_1_1101"
+}

modules/nf-core/bcl2fastq/tests/tags.yml

@@ -0,0 +1,2 @@
+bcl2fastq:
+  - modules/nf-core/bcl2fastq/**

modules/nf-core/bclconvert/tests/main.nf.test

@@ -0,0 +1,41 @@
+nextflow_process {
+
+    name "Test Process BCLCONVERT"
+    script "../main.nf"
+    process "BCLCONVERT"
+    config "./nextflow.config"
+    tag "bclconvert"
+    tag "modules"
+    tag "modules_nfcore"
+
+    test("homo sapiens illumina [bcl]") {
+        when {
+            process {
+                //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996
+                """
+                input[0] = [
+                    [ id: 'test', lane:1 ],
+                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.reports,
+                    process.out.versions,
+                    process.out.fastq,
+                    process.out.undetermined,
+                    file(process.out.logs.get(0).get(1)).list().sort(),
+                    process.out.interop.get(0).get(1).findAll { file(it).name != "IndexMetricsOut.bin" },
+                    ).match()
+                },
+                { assert file(process.out.interop.get(0).get(1).find { file(it).name == "IndexMetricsOut.bin" }).exists() }
+            )
+        }
+    }
+}

modules/nf-core/bclconvert/tests/nextflow.config

@@ -0,0 +1,10 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args = {[
+        meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
+        "--force",
+        "--first-tile-only true"
+    ].join(" ").trim()}
+}

modules/nf-core/bclconvert/tests/tags.yml

@@ -0,0 +1,2 @@
+bclconvert:
+  - modules/nf-core/bclconvert/**

tests/config/pytest_modules.yml

@@ -331,16 +331,6 @@ bcftools/view:
   - modules/nf-core/bcftools/view/**
   - tests/modules/nf-core/bcftools/view/**
 
-bcl2fastq:
-  - modules/nf-core/bcl2fastq/**
-  - modules/nf-core/untar/**
-  - tests/modules/nf-core/bcl2fastq/**
-
-bclconvert:
-  - modules/nf-core/bclconvert/**
-  - modules/nf-core/untar/**
-  - tests/modules/nf-core/bclconvert/**
-
 beagle5/beagle:
   - modules/nf-core/beagle5/beagle/**
   - tests/modules/nf-core/beagle5/beagle/**