mtmalign/align - clean tests and fix output (nf-core#6684)

* clean * Update modules/nf-core/mtmalign/align/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * update align --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
herpov · Oct 2, 2024 · 7aa5ee6 · 7aa5ee6
1 parent 4c08524
commit 7aa5ee6
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Showing 3 changed files with 85 additions and 38 deletions.
diff --git a/modules/nf-core/mtmalign/align/main.nf b/modules/nf-core/mtmalign/align/main.nf
@@ -37,18 +37,16 @@ process MTMALIGN_ALIGN {
 
     mtm-align -i input_list.txt -o ${prefix}.pdb
     # -o does not affect the fasta naming, so move it to the new name
-    mv ./mTM_result/result.fasta ./mTM_result/${prefix}.aln
+    mv ./mTM_result/result.fasta ${prefix}.aln
+    mv ./mTM_result/${prefix}.pdb ${prefix}.pdb
     # Remove ".pdb" from the ids in the alignment file
-    sed -i 's/\\.pdb//g' ./mTM_result/${prefix}.aln
+    sed -i 's/\\.pdb//g' ${prefix}.aln
 
     # compress both output files
     if ${compress}; then
-        pigz -p ${task.cpus} ./mTM_result/${prefix}.aln ./mTM_result/${prefix}.pdb
+        pigz -p ${task.cpus} ${prefix}.aln ${prefix}.pdb
     fi
 
-    # move everything in mTM_result to the working directory
-    mv ./mTM_result/* .
-
     # mtm-align -v prints the wrong version 20180725, so extract it from the cosmetic output in the help message
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test b/modules/nf-core/mtmalign/align/tests/main.nf.test
@@ -9,19 +9,20 @@ nextflow_process {
         tag "mtmalign/align"
         tag "untar"
 
-        test("Test on seatoxin dataset - uncompressed") {
-            setup {
+        setup {
 
-                run("UNTAR") {
-                    script "../../../../../modules/nf-core/untar/main.nf"
-                        process {
-                            """
-                                archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
-                                input[0] = Channel.of(tuple([id:'test'], archive))
-                            """
-                        }
-                }
+            run("UNTAR") {
+                script "../../../../../modules/nf-core/untar/main.nf"
+                    process {
+                        """
+                            archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                            input[0] = Channel.of(tuple([id:'test'], archive))
+                        """
+                    }
             }
+        }
+
+        test("seatoxin - uncompressed") {
 
             when {
                 params {
@@ -49,19 +50,7 @@ nextflow_process {
             }
         }
 
-        test("Test on seatoxin dataset - compressed") {
-            setup {
-
-                run("UNTAR") {
-                    script "../../../../../modules/nf-core/untar/main.nf"
-                        process {
-                            """
-                                archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
-                                input[0] = Channel.of(tuple([id:'test'], archive))
-                            """
-                        }
-                }
-            }
+        test("seatoxin - compressed") {
 
             when {
                 params {
@@ -87,4 +76,27 @@ nextflow_process {
                     )
             }
         }
+
+        test("seatoxin - uncompressed - stub") {
+
+            options '-stub'
+            when {
+                params {
+                }
+                process {
+                    """
+                        input[0] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(dir).listFiles().collect()]}
+                        input[1] = false
+                    """
+                }
+            }
+
+            then {
+                assertAll(
+                    { assert process.success  },
+                    { assert snapshot(process.out).match() }
+                    )
+            }
+        }
+
 }
diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap
@@ -5,10 +5,6 @@
                 "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10"
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
         "timestamp": "2024-06-03T11:01:13.729263689"
     },
     "versions1": {
@@ -17,10 +13,51 @@
                 "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10"
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
         "timestamp": "2024-06-03T11:01:37.28539854"
+    },
+    "seatoxin - uncompressed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pdb:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "structure": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pdb:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10"
+                ]
+            }
+        ],
+        "timestamp": "2024-09-23T16:51:04.027375"
     }
 }