add more module to msa_alignment

classes/msa_alignment.yml

@@ -47,6 +47,8 @@ components:
     - magus/align
     - muscle5/super5
     - tcoffee/align # Needs an argument to return the alignment in fasta
+    - tcoffee/regressive
+    - upp/align
 testdata:
   - - "[ id:'test' ]"
     - "file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true)"

subworkflows/mirpedrol/msa_alignment/main.nf

@@ -5,6 +5,8 @@ include { LEARNMSA_ALIGN } from '../../../modules/nf-core/learnmsa/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'
+include { TCOFFEE_REGRESSIVE } from '../../../modules/nf-core/tcoffee/regressive/main'
+include { UPP_ALIGN } from '../../../modules/nf-core/upp/align/main'
 
 
 workflow MSA_ALIGNMENT {
@@ -33,6 +35,10 @@ workflow MSA_ALIGNMENT {
                     return [ meta, fasta ]
                 tcoffee_align: tool == "tcoffee_align"
                     return [ meta, fasta ]
+                tcoffee_regressive: tool == "tcoffee_regressive"
+                    return [ meta, fasta ]
+                upp_align: tool == "upp_align"
+                    return [ meta, fasta ]
         }
         .set { ch_fasta_branch }
 
@@ -64,6 +70,14 @@ workflow MSA_ALIGNMENT {
     ch_out_alignment = ch_out_alignment.mix(TCOFFEE_ALIGN.out.alignment)
     ch_out_versions = ch_out_versions.mix(TCOFFEE_ALIGN.out.versions)
 
+    TCOFFEE_REGRESSIVE( ch_fasta_branch.tcoffee_regressive, [[], []], [[], [], []], [] )
+    ch_out_alignment = ch_out_alignment.mix(TCOFFEE_REGRESSIVE.out.alignment)
+    ch_out_versions = ch_out_versions.mix(TCOFFEE_REGRESSIVE.out.versions)
+
+    UPP_ALIGN( ch_fasta_branch.upp_align, [[], []], [] )
+    ch_out_alignment = ch_out_alignment.mix(UPP_ALIGN.out.alignment)
+    ch_out_versions = ch_out_versions.mix(UPP_ALIGN.out.versions)
+
 
 
     emit:

subworkflows/mirpedrol/msa_alignment/meta.yml

@@ -17,6 +17,10 @@ components:
       git_remote: "https://github.com/nf-core/modules.git"
   - tcoffee/align:
       git_remote: "https://github.com/nf-core/modules.git"
+  - tcoffee/regressive:
+      git_remote: "https://github.com/nf-core/modules.git"
+  - upp/align:
+      git_remote: "https://github.com/nf-core/modules.git"
 
 input:
   - ch_fasta:

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

@@ -14,6 +14,8 @@ nextflow_workflow {
     tag "subworkflows/../../modules/nf-core/magus/align"
     tag "subworkflows/../../modules/nf-core/muscle5/super5"
     tag "subworkflows/../../modules/nf-core/tcoffee/align"
+    tag "subworkflows/../../modules/nf-core/tcoffee/regressive"
+    tag "subworkflows/../../modules/nf-core/upp/align"
 
     config './nextflow.config'
 
@@ -108,7 +110,6 @@ nextflow_workflow {
                 { assert path(workflow.out.alignment[0][1]).getText().contains("1sh1") },
                 { assert path(workflow.out.alignment[0][1]).getText().contains("1apf") },
                 { assert path(workflow.out.alignment[0][1]).getText().contains("1ahl") },
-                { assert snapshot(workflow.out.versions).match("magus/align") },
             )
         }
     }
@@ -149,5 +150,41 @@ nextflow_workflow {
         }
     }
 
+    test("tcoffee/regressive") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'tcoffee_regressive'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("tcoffee/regressive") },
+            )
+        }
+    }
+
+    test("upp/align") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'upp_align'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("upp/align") },
+            )
+        }
+    }
+
 
 }

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

@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c74ca8b91c442fc4ea29219ee1b724fd"
+                    "versions.yml:md5,662446ba7a24e755a11692e9302e4895"
                 ],
                 "alignment": [
                     [
@@ -55,7 +55,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c74ca8b91c442fc4ea29219ee1b724fd"
+                    "versions.yml:md5,662446ba7a24e755a11692e9302e4895"
                 ]
             }
         ],
@@ -65,6 +65,39 @@
         },
         "timestamp": "2025-07-31T13:38:19.076634506"
     },
+    "tcoffee/regressive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,919b5de419f7e8355773808305cc9da5"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,919b5de419f7e8355773808305cc9da5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:51:10.271917631"
+    },
     "learnmsa/align - stub": {
         "content": [
             {
@@ -208,5 +241,38 @@
             "nextflow": "25.04.6"
         },
         "timestamp": "2025-08-01T07:27:07.276478754"
+    },
+    "upp/align": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a543b6c4d215628c0307111268496557"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2c5ca42adf5dc958969926ab31eedb2a"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a543b6c4d215628c0307111268496557"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2c5ca42adf5dc958969926ab31eedb2a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:51:18.37628695"
     }
 }

subworkflows/mirpedrol/msa_alignment/tests/nextflow.config

@@ -5,4 +5,7 @@ process {
     withName: 'MSA_ALIGNMENT:TCOFFEE_ALIGN'{
         ext.args = { "-output fasta_aln" }
     }
+    withName: "MSA_ALIGNMENT:UPP_ALIGN" {
+        ext.args = { "-m amino" }
+    }
 }