Swap bbmap/align to nf-test and add stub (nf-core#7278)

* Swap bbmap/align to nf-test * Add missing tag
fellen31 · Jan 10, 2025 · 62b1a43 · 62b1a43
1 parent a14e448
commit 62b1a43
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Showing 9 changed files with 282 additions and 110 deletions.
diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf
@@ -48,6 +48,19 @@ process BBMAP_ALIGN {
         -Xmx${task.memory.toGiga()}g \\
         &> ${prefix}.bbmap.log
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.bbmap.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")

diff --git a/modules/nf-core/bbmap/align/tests/main.nf.test b/modules/nf-core/bbmap/align/tests/main.nf.test
@@ -0,0 +1,171 @@
+nextflow_process {
+
+    name "Test Process BBMAP_ALIGN"
+    script "../main.nf"
+    process "BBMAP_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/align"
+    tag "bbmap/index"
+
+    setup {
+        run("BBMAP_INDEX") {
+            script "../../index/main.nf"
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+    }
+
+    test("paired_end - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+					file(process.out.log[0][1]).name,
+                    process.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5()},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - index") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                input[1] = BBMAP_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+					file(process.out.log[0][1]).name,
+                    process.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5()},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("single_end - index") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                input[1] = BBMAP_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+					file(process.out.log[0][1]).name,
+                    process.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5()},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - index - pigz") {
+        config "./nextflow.config"
+        when {
+            params {
+                module_args = 'unpigz=t'
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                input[1] = BBMAP_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+					file(process.out.log[0][1]).name,
+                    process.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5()},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - index - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                input[1] = BBMAP_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+					file(process.out.log[0][1]).name,
+                    process.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5()},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bbmap/align/tests/main.nf.test.snap b/modules/nf-core/bbmap/align/tests/main.nf.test.snap
@@ -0,0 +1,82 @@
+{
+    "single_end - index": {
+        "content": [
+            "test.bbmap.log",
+            [
+                "c17efa4ccc4e9018090792c71af92660"
+            ],
+            [
+                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T21:06:20.348251263"
+    },
+    "paired_end - index": {
+        "content": [
+            "test.bbmap.log",
+            [
+                "88d78879c34214288644aec7ec3cb270"
+            ],
+            [
+                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T21:06:05.162378558"
+    },
+    "paired_end - fasta": {
+        "content": [
+            "test.bbmap.log",
+            [
+                "88d78879c34214288644aec7ec3cb270"
+            ],
+            [
+                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T21:05:49.658797332"
+    },
+    "paired_end - index - pigz": {
+        "content": [
+            "test.bbmap.log",
+            [
+                "88d78879c34214288644aec7ec3cb270"
+            ],
+            [
+                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T21:06:36.326962674"
+    },
+    "paired_end - index - stub": {
+        "content": [
+            "test.bbmap.log",
+            [
+                "d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T21:06:47.377762689"
+    }
+}
diff --git a/modules/nf-core/bbmap/align/tests/nextflow.config b/modules/nf-core/bbmap/align/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: BBMAP_ALIGN {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf
@@ -26,6 +26,17 @@ process BBMAP_INDEX {
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+    END_VERSIONS
+    """
+    stub:
+    """
+    mkdir -p ref
+    touch ref/info.txt
+    touch ref/summary.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -40,9 +40,6 @@ bamtools/split:
 basicpy:
   - modules/nf-core/basicpy/**
   - tests/modules/nf-core/basicpy/**
-bbmap/align:
-  - modules/nf-core/bbmap/align/**
-  - tests/modules/nf-core/bbmap/align/**
 biohansel:
   - modules/nf-core/biohansel/**
   - tests/modules/nf-core/biohansel/**

diff --git a/tests/modules/nf-core/bbmap/align/main.nf b/tests/modules/nf-core/bbmap/align/main.nf
diff --git a/tests/modules/nf-core/bbmap/align/nextflow.config b/tests/modules/nf-core/bbmap/align/nextflow.config