Swap unzip to nf-test (continuation of 5357) (#5897)

* unzip stub, nf-test, snap * Revert "unzip stub, nf-test, snap" This reverts commit dec35aa. * Reapply "unzip stub, nf-test, snap" This reverts commit e0d708e. * added minimal required tests for process and stub * added snapshot * simplify snapshot input in stub test Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * remove unneeded stub files * migrate pytest for unzipfiles * add snapshot file for script block * added stub * added stub and stub test * updated stub snapshot for unzip * remove unneeded test config * Update snaps and malt * Update malt for linting * Fix linting for maltextract * Swap test-data paths for malt modules * Update modules/nf-core/maltextract/tests/main.nf.test --------- Co-authored-by: Sateesh <perisateesh@gmail.com> Co-authored-by: Jenny Leopoldina Smith <jennyl.smith12@gmail.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
nf-core · Jul 16, 2024 · b0c3ff2 · b0c3ff2
1 parent 96e59e7
commit b0c3ff2
Show file tree

Hide file tree

Showing 22 changed files with 327 additions and 104 deletions.
diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
                 input[1] = []
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """
@@ -45,7 +45,8 @@ nextflow_process {
                         path("${process.out.index[0]}/ref.inf"),
                         path("${process.out.index[0]}/taxonomy.idx"),
                         path("${process.out.index[0]}/taxonomy.map"),
-                        path("${process.out.index[0]}/taxonomy.tre")
+                        path("${process.out.index[0]}/taxonomy.tre"),
+                        process.out.versions
                         )
                     .match()
                 },
@@ -64,7 +65,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
                 input[1] = []
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """

diff --git a/modules/nf-core/malt/build/tests/main.nf.test.snap b/modules/nf-core/malt/build/tests/main.nf.test.snap
@@ -26,6 +26,10 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
         "timestamp": "2024-01-26T11:49:19.685017271"
     },
     "sarscov2 - fastq": {
@@ -36,8 +40,15 @@
             "ref.inf:md5,b146842067cf278ef1d23e6c2e7c0c35",
             "taxonomy.idx:md5,bb335e7c378a5bd85761b6eeed16d984",
             "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0",
-            "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e"
+            "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e",
+            [
+                "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97"
+            ]
         ],
-        "timestamp": "2024-01-26T11:48:45.195850552"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T19:04:45.72181253"
     }
 }
diff --git a/modules/nf-core/malt/run/meta.yml b/modules/nf-core/malt/run/meta.yml
@@ -39,7 +39,7 @@ output:
       type: file
       description: MEGAN6 RMA6 file
       pattern: "*.rma6"
-  - sam:
+  - alignments:
       type: file
       description: Alignment files in Tab, Text or MEGAN-compatible SAM format
       pattern: "*.{tab,txt,sam}"

diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test malt/run
 nextflow_process {
 
     name "Test Process MALT_RUN"
@@ -27,7 +25,7 @@ nextflow_process {
             script "../../../malt/build/main.nf"
             process {
                 """
-                input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
                 input[1] = []
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """
@@ -43,7 +41,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test_1', single_end:false ],
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
                     ]
                 ]
                 input[1] = MALT_BUILD.out.index
@@ -56,6 +54,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                         process.out.alignments,
+                        process.out.versions,
                         file(process.out.rma6[0][1]).name
                     ).match()
                 },
@@ -75,7 +74,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test_1', single_end:false ],
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
                     ]
                 ]
                 input[1] = MALT_BUILD.out.index

diff --git a/modules/nf-core/malt/run/tests/main.nf.test.snap b/modules/nf-core/malt/run/tests/main.nf.test.snap
@@ -64,6 +64,10 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
         "timestamp": "2024-01-26T14:15:43.18685293"
     },
     "sarscov2 - fastq": {
@@ -77,8 +81,15 @@
                     "test_1.blastn.sam.gz:md5,8ad56803c1674e1a8cd42fe8801e71fd"
                 ]
             ],
+            [
+                "versions.yml:md5,5b91a785e0342f9ef17a634c0452335a"
+            ],
             "test_1.rma6"
         ],
-        "timestamp": "2024-01-26T14:15:08.880645244"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T07:04:07.674069223"
     }
 }
diff --git a/modules/nf-core/maltextract/tests/main.nf.test b/modules/nf-core/maltextract/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 script "../../unzip/main.nf"
                 process {
                     """
-                    input[0] = [[], file('https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip')]
+                    input[0] = [[], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip')]
                     """
                 }
             }
@@ -25,8 +25,9 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [], // meta map
-                file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/malt/test.rma6') ]
-                input[1] = file('https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt')
+                    file(params.modules_testdata_base_path + 'delete_me/malt/test.rma6')
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/maltextract/taxon_list.txt')
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """
             }
@@ -35,12 +36,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match('version') },
-                // snapshots dont work, because the results channel contains a log file that changes with each run
                 { assert snapshot(
-                        path("${process.out.results.get(0).get(1)}/ScanSummary.txt"),
-                    ).match('results')
-                }
+                    process.out.versions,
+                    path("${process.out.results.get(0).get(1)}/ScanSummary.txt")
+                ).match() },
             )
         }
     }

diff --git a/modules/nf-core/maltextract/tests/main.nf.test.snap b/modules/nf-core/maltextract/tests/main.nf.test.snap
@@ -1,24 +1,15 @@
 {
-    "version": {
+    "test_maltextract": {
         "content": [
             [
                 "versions.yml:md5,4d87de5def1287321effde6545901cf6"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
-        "timestamp": "2024-03-19T13:58:17.979106"
-    },
-    "results": {
-        "content": [
+            ],
             "ScanSummary.txt:md5,209fb35426f6a459db0f4af0dc544b10"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-19T14:03:56.643826"
+        "timestamp": "2024-07-01T08:19:20.696046683"
     }
 }
diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf
@@ -20,7 +20,6 @@ process UNZIP {
     script:
     def args = task.ext.args ?: ''
     if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
-
     prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
     """
     7za \\
@@ -34,4 +33,17 @@ process UNZIP {
         7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
+    prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
+    """
+    mkdir "${prefix}"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/unzip/tests/main.nf.test b/modules/nf-core/unzip/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process UNZIP"
+    script "../main.nf"
+    process "UNZIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "unzip"
+
+    test("generic [tar] [tar_gz]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id: 'hello' ],
+                            file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+          )
+        }
+    }
+
+    test("generic [tar] [tar_gz] stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id: 'hello' ],
+                            file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/unzip/tests/main.nf.test.snap b/modules/nf-core/unzip/tests/main.nf.test.snap
@@ -0,0 +1,76 @@
+{
+    "generic [tar] [tar_gz] stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8"
+                ],
+                "unzipped_archive": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T19:16:37.11550986"
+    },
+    "generic [tar] [tar_gz]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        [
+                            "hello.tar:md5,80c66db79a773bc87b3346035ff9593e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8"
+                ],
+                "unzipped_archive": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        [
+                            "hello.tar:md5,80c66db79a773bc87b3346035ff9593e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T19:16:25.120242571"
+    }
+}
diff --git a/modules/nf-core/unzip/tests/tags.yml b/modules/nf-core/unzip/tests/tags.yml
@@ -0,0 +1,2 @@
+unzip:
+  - "modules/nf-core/unzip/**"
diff --git a/modules/nf-core/unzipfiles/main.nf b/modules/nf-core/unzipfiles/main.nf
@@ -34,4 +34,16 @@ process UNZIPFILES {
         7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
+    """
+    mkdir "${prefix}"
+    touch "${prefix}/hello.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
+    END_VERSIONS
+    """
 }