Tcoffee stub tests (#6555)

* Fix align module test * Fix nf-tests * update typos * Update snaps * Update modules/nf-core/tcoffee/align/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/align/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/alncompare/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * update tetss * update tests align * update tests * update irmsd test * Update modules/nf-core/tcoffee/align/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/alncompare/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/irmsd/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/irmsd/tests/main.nf.test Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/seqreformat/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/tcs/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Update modules/nf-core/tcoffee/tcs/meta.yml Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * remove changes in consensus * fix * update snap * add * add tree test * rerun * test * test --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>
nf-core · Sep 18, 2024 · 6453bce · 6453bce
1 parent ba8aac9
commit 6453bce
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Showing 23 changed files with 421 additions and 339 deletions.
diff --git a/modules/nf-core/fastme/tests/main.nf.test.snap b/modules/nf-core/fastme/tests/main.nf.test.snap
@@ -54,10 +54,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:03:04.842045"
     },
     "versions": {
@@ -66,10 +62,6 @@
                 "versions.yml:md5,0e7f28ae349efffa1ef75c2279e975b6"
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:58.72899"
     },
     "stats_boot": {
@@ -90,10 +82,6 @@
                 ""
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:09:35.813028"
     },
     "setoxin - phylip - with_tree": {
@@ -151,10 +139,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:51.77025"
     },
     "setoxin - phylip - basic": {
@@ -212,10 +196,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:44.598308"
     }
 }
diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
@@ -57,6 +57,8 @@ process TCOFFEE_ALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch ${prefix}.aln${compress ? '.gz':''}
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test
@@ -11,15 +11,15 @@ nextflow_process {
     tag "famsa/guidetree"
     tag "untar"
 
-    test("fasta - align_sequence") {
+    test("align_sequence - compressed - seatoxin") {
 
         config "./sequence.config"
 
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -31,21 +31,21 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment")},
-                { assert snapshot(process.out.versions).match("versions_uncomp") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
             )
         }
     }
 
-    test("fasta - align_sequence - uncompressed") {
+    test("align_sequence - uncompressed - seatoxin") {
 
         config "./sequence.config"
 
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -57,13 +57,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment - uncompressed")},
-                { assert snapshot(process.out.versions).match("versions_comp") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") },
             )
         }
     }
 
-    test("sarscov2 - fasta - align_with_guide_tree") {
+    test("align_with_guide_tree - uncompressed - seatoxin") {
 
         config "./tree.config"
 
@@ -74,7 +74,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                                ]
 
                     """
@@ -86,7 +86,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]}
                 input[2] = [ [:], [], [] ]
@@ -98,14 +98,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment_guidetree")},
-                { assert snapshot(process.out.versions).match("versions_guidetree") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
             )
         }
 
     }
 
-    test("fasta - align_with_structure") {
+    test("align_with_structure - uncompressed - seatoxin") {
 
         config "./structure.config"
 
@@ -116,7 +116,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                                 file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                                 file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
                                ]
 
                     """
@@ -128,7 +128,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [ [:], [] ]
                 input[2] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], [] ,file(dir).listFiles().collect()]}
@@ -148,15 +148,15 @@ nextflow_process {
 
     }
 
-    test("fasta - align_with_lib") {
+    test("align_with_lib - seatoxin") {
 
         config "./lib.config"
 
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -168,10 +168,40 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment - lib") },
-                { assert path(process.out.lib.get(0).get(1)).getText().contains("1ahl") },
-                { assert snapshot(process.out.versions).match("versions_lib") }
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
+                { assert snapshot(process.out.versions).match()
+                }
             )
         }
     }
+
+    test("align_sequence - uncompressed - seatoxin - stub") {
+        options "-stub"
+        config "./sequence.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = [[:],[],[]]
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.alignment,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
@@ -6,125 +6,77 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
         "timestamp": "2024-02-28T19:00:28.712838"
     },
-    "versions_lib": {
+    "align_sequence - uncompressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T14:04:06.031557"
+        "timestamp": "2024-09-16T10:38:34.006567221"
     },
-    "alignment - uncompressed": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln:md5,bd1db08ad04514cc6d1334598c1a6ef0"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:54.582504"
-    },
-    "versions_comp": {
+    "align_sequence - compressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T18:59:54.593312"
+        "timestamp": "2024-09-16T10:38:18.99603304"
     },
-    "versions_guidetree": {
+    "align_with_guide_tree - uncompressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T19:00:10.618213"
+        "timestamp": "2024-09-16T10:38:48.044669392"
     },
-    "alignment - lib": {
+    "align_with_lib - seatoxin": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
-                ]
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T13:57:39.653762"
+        "timestamp": "2024-09-16T10:47:34.909457138"
     },
-    "alignment": {
+    "align_sequence - uncompressed - seatoxin - stub": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
+                    "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:35.169119"
-    },
-    "versions_uncomp": {
-        "content": [
+            ],
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:35.2062"
-    },
-    "alignment_guidetree": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln.gz:md5,93bc8adfcd88f7913718eacc13da8e4a"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T19:00:10.611489"
+        "timestamp": "2024-09-16T12:55:10.267649283"
     }
 }