add more module to msa_treealign

classes/msa_treealign.yml

@@ -52,6 +52,8 @@ components:
     - famsa/align
     - magus/align
     - tcoffee/align
+    - 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_treealign/main.nf

@@ -2,6 +2,8 @@ include { CLUSTALO_ALIGN } from '../../../modules/nf-core/clustalo/align/main'
 include { FAMSA_ALIGN } from '../../../modules/nf-core/famsa/align/main'
 include { MAGUS_ALIGN } from '../../../modules/nf-core/magus/align/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_TREEALIGN {
@@ -25,6 +27,10 @@ workflow MSA_TREEALIGN {
                     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 }
     ch_tree
@@ -38,6 +44,10 @@ workflow MSA_TREEALIGN {
                     return [ meta, tree ]
                 tcoffee_align: tool == "tcoffee_align"
                     return [ meta, tree ]
+                tcoffee_regressive: tool == "tcoffee_regressive"
+                    return [ meta, tree ]
+                upp_align: tool == "upp_align"
+                    return [ meta, tree ]
         }
         .set { ch_tree_branch }
 
@@ -57,6 +67,14 @@ workflow MSA_TREEALIGN {
     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_tree_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_tree_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_treealign/meta.yml

@@ -11,6 +11,10 @@ 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_treealign/msa_treealign.diff

@@ -0,0 +1,19 @@
+Changes in component 'mirpedrol/msa_treealign'
+'subworkflows/mirpedrol/msa_treealign/.nf-test.log' was created
+'subworkflows/mirpedrol/msa_treealign/meta.yml' is unchanged
+'subworkflows/mirpedrol/msa_treealign/main.nf' is unchanged
+'subworkflows/mirpedrol/msa_treealign/tests/main.nf.test.snap' was created
+'subworkflows/mirpedrol/msa_treealign/tests/nextflow.config' was created
+Changes in 'msa_treealign/tests/main.nf.test':
+--- subworkflows/mirpedrol/msa_treealign/tests/main.nf.test
++++ subworkflows/mirpedrol/msa_treealign/tests/main.nf.test
+@@ -111,6 +111,7 @@
+     }
+
+     test("upp/align") {
++        config "./nextflow.config"
+
+         when {
+             workflow {
+
+************************************************************

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

@@ -11,6 +11,8 @@ nextflow_workflow {
     tag "subworkflows/../../modules/nf-core/famsa/align"
     tag "subworkflows/../../modules/nf-core/magus/align"
     tag "subworkflows/../../modules/nf-core/tcoffee/align"
+    tag "subworkflows/../../modules/nf-core/tcoffee/regressive"
+    tag "subworkflows/../../modules/nf-core/upp/align"
 
 
     test("clustalo/align") {
@@ -89,5 +91,44 @@ 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'] )
+                input[1] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.dnd', checkIfExists: true), 'tcoffee_regressive'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("tcoffee/regressive") },
+            )
+        }
+    }
+
+    test("upp/align") {
+        config "./nextflow.config"
+
+        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'] )
+                input[1] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.dnd', checkIfExists: true), 'upp_align'] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("upp/align") },
+            )
+        }
+    }
+
 
 }

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

@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,dc23c65f66a62f337556459f11efb7b3"
+                    "versions.yml:md5,a1ee55248052d51e7dea2c7ae59d27d7"
                 ],
                 "alignment": [
                     [
@@ -55,7 +55,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,dc23c65f66a62f337556459f11efb7b3"
+                    "versions.yml:md5,a1ee55248052d51e7dea2c7ae59d27d7"
                 ]
             }
         ],
@@ -65,6 +65,40 @@
         },
         "timestamp": "2025-08-01T14:08:10.972913645"
     },
+    "tcoffee/regressive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
+                    ]
+
+                ],
+                "1": [
+                    "versions.yml:md5,167b47da97b1e1b8f168aa85495245b4"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,167b47da97b1e1b8f168aa85495245b4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:48:00.884458852"
+    },
     "magus/align": {
         "content": [
             {
@@ -130,5 +164,38 @@
             "nextflow": "25.04.6"
         },
         "timestamp": "2025-08-01T14:09:48.216260207"
+    },
+    "upp/align": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a543b6c4d215628c0307111268496557"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,480e12b84ba1a750dc9e347a0ee77d1b"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,a543b6c4d215628c0307111268496557"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,480e12b84ba1a750dc9e347a0ee77d1b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:48:08.969096652"
     }
-}
+}

subworkflows/mirpedrol/msa_treealign/tests/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    withName: "UPP_ALIGN" {
+        ext.args = { "-m amino" }
+    }
+
+}