stubs and test for rnaseq modules - part I (#5854)

* stubs and test for bbmap_bbsplit * add test for index * add stubs for custom/catadditionalfasta * add stubs for fq/subsample * add stubs for hisat2/extractsplicesites * update fastq_align_hisat2 snapshot * add stubs for hisat2/build * add stubs for hisat2/align * more stubs bbmap/bbsplit * add stubs for preseq/lcextrap * more stubs for fq/subsample * proper stubs for hisat2/align * remove old snaps
nf-core · Jun 21, 2024 · 2c6b114 · 2c6b114
1 parent 6c2309a
commit 2c6b114
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Showing 22 changed files with 1,744 additions and 62 deletions.
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -105,4 +105,23 @@ process BBMAP_BBSPLIT {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def other_refs = ''
+    other_ref_names.eachWithIndex { name, index ->
+        other_refs += "echo '' | gzip > ${prefix}_primary_${name}.fastq.gz"
+    }
+    """
+    mkdir bbsplit
+
+    echo '' | gzip >  ${prefix}_primary.fastq.gz
+    ${other_refs}
+    touch ${prefix}.stats.txt
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
@@ -8,6 +8,66 @@ nextflow_process {
     tag "bbmap"
     tag "bbmap/bbsplit"
 
+    test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [[:],[]]
+                input[1] = []
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[3] = Channel.of([
+                    [ 'human' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                ])
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.index[0]}").exists() },
+                { assert path(process.out.log[0][1]).text.contains("No index available") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta - index - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [[:],[]]
+                input[1] = []
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[3] = Channel.of([
+                    [ 'human' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                ])
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("sarscov2_se_fastq_fasta_chr22_fasta") {
 
         setup {
@@ -88,4 +148,37 @@ nextflow_process {
             )
         }
     }
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                    input[0] = Channel.of([
+                        [ 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] = []
+                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                    input[3] = Channel.of([
+                        [ 'human' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                    ])
+                    input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
@@ -26,5 +26,231 @@
             "nextflow": "23.10.1"
         },
         "timestamp": "2024-02-01T17:11:22.441753642"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - index": {
+        "content": [
+            [
+                "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T16:41:29.784895"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - index - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+
+                        },
+                        [
+                            "null_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "null_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+
+                        },
+                        [
+                            "null_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "null_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+
+                        },
+                        "null.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+
+                        },
+                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ],
+                "all_fastq": [
+                    [
+                        {
+
+                        },
+                        [
+                            "null_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "null_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "index": [
+                    [
+
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+
+                        },
+                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "primary_fastq": [
+                    [
+                        {
+
+                        },
+                        [
+                            "null_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "null_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+
+                        },
+                        "null.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T18:49:27.280432"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ],
+                "all_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "index": [
+                    [
+
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "primary_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T16:16:05.793544"
     }
-}
+}
diff --git a/modules/nf-core/custom/catadditionalfasta/main.nf b/modules/nf-core/custom/catadditionalfasta/main.nf
@@ -21,4 +21,17 @@ process CUSTOM_CATADDITIONALFASTA {
 
     script:
     template 'fasta2gtf.py'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir out
+    touch out/genome_transcriptome.fasta
+    touch out/genome_transcriptome.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | grep -v "Python ")
+    END_VERSIONS
+    """
 }