add mafft/align module to msa_alignment class

classes/msa_alignment.yml

@@ -43,7 +43,7 @@ components:
     - famsa/align
     - kalign/align
     - learnmsa/align
-    #- mafft/align # Multiple inputs - to fix upstream
+    - mafft/align # Multiple inputs
     - magus/align
     - muscle5/super5
     - tcoffee/align # Needs an argument to return the alignment in fasta

subworkflows/mirpedrol/msa_alignment/main.nf

@@ -2,6 +2,7 @@ include { CLUSTALO_ALIGN } from '../../../modules/nf-core/clustalo/align/main'
 include { FAMSA_ALIGN } from '../../../modules/nf-core/famsa/align/main'
 include { KALIGN_ALIGN } from '../../../modules/nf-core/kalign/align/main'
 include { LEARNMSA_ALIGN } from '../../../modules/nf-core/learnmsa/align/main'
+include { MAFFT_ALIGN } from '../../../modules/nf-core/mafft/align/main'
 include { MAGUS_ALIGN } from '../../../modules/nf-core/magus/align/main'
 include { MUSCLE5_SUPER5 } from '../../../modules/nf-core/muscle5/super5/main'
 include { TCOFFEE_ALIGN } from '../../../modules/nf-core/tcoffee/align/main'
@@ -27,6 +28,8 @@ workflow MSA_ALIGNMENT {
                     return [ meta, fasta ]
                 learnmsa_align: tool == "learnmsa_align"
                     return [ meta, fasta ]
+                mafft_align: tool == "mafft_align"
+                    return [ meta, fasta ]
                 magus_align: tool == "magus_align"
                     return [ meta, fasta ]
                 muscle5_super5: tool == "muscle5_super5"
@@ -52,6 +55,10 @@ workflow MSA_ALIGNMENT {
     ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment)
     ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions)
 
+    MAFFT_ALIGN( ch_fasta_branch.mafft_align, [[], []], [[], []], [[], []], [[], []], [[], []], [] )
+    ch_out_alignment = ch_out_alignment.mix(MAFFT_ALIGN.out.fas)
+    ch_out_versions = ch_out_versions.mix(MAFFT_ALIGN.out.versions)
+
     MAGUS_ALIGN( ch_fasta_branch.magus_align, [[], []], [] )
     ch_out_alignment = ch_out_alignment.mix(MAGUS_ALIGN.out.alignment)
     ch_out_versions = ch_out_versions.mix(MAGUS_ALIGN.out.versions)

subworkflows/mirpedrol/msa_alignment/meta.yml

@@ -11,6 +11,8 @@ components:
       git_remote: "https://github.com/nf-core/modules.git"
   - learnmsa/align:
       git_remote: "https://github.com/nf-core/modules.git"
+  - mafft/align:
+      git_remote: "https://github.com/nf-core/modules.git"
   - magus/align:
       git_remote: "https://github.com/nf-core/modules.git"
   - muscle5/super5:

subworkflows/mirpedrol/msa_alignment/msa_alignment.diff

@@ -1,30 +1,42 @@
 Changes in component 'mirpedrol/msa_alignment'
 'subworkflows/mirpedrol/msa_alignment/meta.yml' is unchanged
-'subworkflows/mirpedrol/msa_alignment/main.nf' is unchanged
+Changes in 'msa_alignment/main.nf':
+--- subworkflows/mirpedrol/msa_alignment/main.nf
++++ subworkflows/mirpedrol/msa_alignment/main.nf
+@@ -55,7 +55,7 @@
+     ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment)
+     ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions)
+
+-    MAFFT_ALIGN( ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, [] )
++    MAFFT_ALIGN( ch_fasta_branch.mafft_align, [[], []], [[], []], [[], []], [[], []], [[], []], [] )
+     ch_out_alignment = ch_out_alignment.mix(MAFFT_ALIGN.out.fas)
+     ch_out_versions = ch_out_versions.mix(MAFFT_ALIGN.out.versions)
+
+
 'subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap' was created
 'subworkflows/mirpedrol/msa_alignment/tests/nextflow.config' was created
 Changes in 'msa_alignment/tests/main.nf.test':
 --- subworkflows/mirpedrol/msa_alignment/tests/main.nf.test
 +++ subworkflows/mirpedrol/msa_alignment/tests/main.nf.test
-@@ -15,6 +15,7 @@
+@@ -16,6 +16,7 @@
      tag "subworkflows/../../modules/nf-core/muscle5/super5"
      tag "subworkflows/../../modules/nf-core/tcoffee/align"
-
+ 
 +    config './nextflow.config'
-
+ 
      test("clustalo/align") {
-
-@@ -70,7 +71,8 @@
+ 
+@@ -71,7 +72,8 @@
          }
      }
-
+ 
 -    test("learnmsa/align") {
 +    test("learnmsa/align - stub") {
 +        options "-stub"
-
+ 
          when {
              workflow {
-@@ -83,7 +85,7 @@
+@@ -84,7 +86,7 @@
          then {
              assertAll(
                  { assert workflow.success },
@@ -33,7 +45,7 @@ Changes in 'msa_alignment/tests/main.nf.test':
              )
          }
      }
-@@ -101,7 +103,12 @@
+@@ -120,7 +122,12 @@
          then {
              assertAll(
                  { assert workflow.success },

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

@@ -11,6 +11,7 @@ nextflow_workflow {
     tag "subworkflows/../../modules/nf-core/famsa/align"
     tag "subworkflows/../../modules/nf-core/kalign/align"
     tag "subworkflows/../../modules/nf-core/learnmsa/align"
+    tag "subworkflows/../../modules/nf-core/mafft/align"
     tag "subworkflows/../../modules/nf-core/magus/align"
     tag "subworkflows/../../modules/nf-core/muscle5/super5"
     tag "subworkflows/../../modules/nf-core/tcoffee/align"
@@ -90,6 +91,24 @@ nextflow_workflow {
         }
     }
 
+    test("mafft/align") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'mafft_align'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("mafft/align") },
+            )
+        }
+    }
+
     test("magus/align") {
 
         when {

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

@@ -131,6 +131,39 @@
         },
         "timestamp": "2025-08-01T07:01:54.454247483"
     },
+    "mafft/align": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                            "test.fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4eac1bd98ea7280bd9822cc13631b619"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4eac1bd98ea7280bd9822cc13631b619"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-08-20T14:48:11.902561829"
+    },
     "magus/align": {
         "content": [
             [