add more module to msa_guidetree

.github/workflows/test.yml

@@ -26,7 +26,7 @@ jobs:
         uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6
         with:
           head: ${{ github.sha }}
-          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
+          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha || 'origin/main' }}
           n_parents: 0
 
       - name: Select subworkflows

classes/msa_guidetree.yml

@@ -43,6 +43,7 @@ components:
     - clustalo/guidetree
     - famsa/guidetree
     - magus/guidetree
+    - mafft/guidetree
 testdata:
   - - "[ id:'test' ]"
     - "file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true)"

subworkflows/mirpedrol/msa_guidetree/main.nf

@@ -1,6 +1,7 @@
 include { CLUSTALO_GUIDETREE } from '../../../modules/nf-core/clustalo/guidetree/main'
 include { FAMSA_GUIDETREE } from '../../../modules/nf-core/famsa/guidetree/main'
 include { MAGUS_GUIDETREE } from '../../../modules/nf-core/magus/guidetree/main'
+include { MAFFT_GUIDETREE } from '../../../modules/nf-core/mafft/guidetree/main'
 
 
 workflow MSA_GUIDETREE {
@@ -21,6 +22,8 @@ workflow MSA_GUIDETREE {
                     return [ meta, fasta ]
                 magus_guidetree: tool == "magus_guidetree"
                     return [ meta, fasta ]
+                mafft_guidetree: tool == "mafft_guidetree"
+                    return [ meta, fasta ]
         }
         .set { ch_fasta_branch }
 
@@ -36,6 +39,10 @@ workflow MSA_GUIDETREE {
     ch_out_tree = ch_out_tree.mix(MAGUS_GUIDETREE.out.tree)
     ch_out_versions = ch_out_versions.mix(MAGUS_GUIDETREE.out.versions)
 
+    MAFFT_GUIDETREE( ch_fasta_branch.mafft_guidetree )
+    ch_out_tree = ch_out_tree.mix(MAFFT_GUIDETREE.out.tree)
+    ch_out_versions = ch_out_versions.mix(MAFFT_GUIDETREE.out.versions)
+
 
 
     emit:

subworkflows/mirpedrol/msa_guidetree/meta.yml

@@ -9,6 +9,8 @@ components:
       git_remote: "https://github.com/nf-core/modules.git"
   - magus/guidetree:
       git_remote: "https://github.com/nf-core/modules.git"
+  - mafft/guidetree:
+      git_remote: "https://github.com/nf-core/modules.git"
 
 input:
   - ch_fasta:

subworkflows/mirpedrol/msa_guidetree/tests/main.nf.test

@@ -10,6 +10,7 @@ nextflow_workflow {
     tag "subworkflows/../../modules/nf-core/clustalo/guidetree"
     tag "subworkflows/../../modules/nf-core/famsa/guidetree"
     tag "subworkflows/../../modules/nf-core/magus/guidetree"
+    tag "subworkflows/../../modules/nf-core/mafft/guidetree"
 
 
     test("clustalo/guidetree") {
@@ -66,7 +67,24 @@ nextflow_workflow {
                 { assert path(workflow.out.tree[0][1]).getText().contains("1sh1") },
                 { assert path(workflow.out.tree[0][1]).getText().contains("1apf") },
                 { assert path(workflow.out.tree[0][1]).getText().contains("1ahl") },
-                { assert snapshot(workflow.out.versions).match("magus/guidetree") },
+            )
+        }
+    }
+
+    test("mafft/guidetree") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'mafft_guidetree'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("mafft/guidetree") },
             )
         }
     }

subworkflows/mirpedrol/msa_guidetree/tests/main.nf.test.snap

@@ -32,6 +32,39 @@
         },
         "timestamp": "2025-08-01T12:21:33.436132015"
     },
+    "mafft/guidetree": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dnd:md5,f3510ecc52655e1827658396aec90b24"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,995c0bd161578e9d638264659f5e55b5"
+                ],
+                "tree": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dnd:md5,f3510ecc52655e1827658396aec90b24"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,995c0bd161578e9d638264659f5e55b5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:46:56.709060689"
+    },
     "clustalo/guidetree": {
         "content": [
             {
@@ -77,4 +110,4 @@
         },
         "timestamp": "2025-08-19T13:46:43.306273138"
     }
-}
+}