Unify msa modules

modules/nf-core/tcoffee/align/main.nf

@@ -23,12 +23,13 @@ process TCOFFEE_ALIGN {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def tree_args = tree ? "-usetree $tree" : ""
-    def template_args = template ? "-template_file $template" : ""
-    def outfile = compress ? "stdout" : "${prefix}.aln"
-    def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.aln.gz" : ""
+    def args               = task.ext.args ?: ''
+    def prefix             = task.ext.prefix ?: "${meta.id}"
+    def tree_args          = tree ? "-usetree $tree" : ""
+    def template_args      = template ? "-template_file $template" : ""
+    def outfile            = compress ? "stdout" : "${prefix}.aln"
+    def default_out_format = ("-output" in "${args}") ? "" : "-output fasta_aln"
+    def write_output       = compress ? " | pigz -cp ${task.cpus} > ${prefix}.aln.gz" : ""
     """
     export TEMP='./'
     export TMP_4_TCOFFEE="./"
@@ -37,6 +38,7 @@ process TCOFFEE_ALIGN {
         $tree_args \
         $template_args \
         $args \
+        $default_out_format \
         -thread ${task.cpus} \
         -outfile $outfile \
         $write_output

modules/nf-core/tcoffee/align/tests/lib.config

@@ -1,3 +1,3 @@
 process {
-    ext.args = { "-output fasta_aln -out_lib=sample_lib1.tc_lib" }
+    ext.args = { "-out_lib=sample_lib1.tc_lib" }
 }

modules/nf-core/tcoffee/align/tests/main.nf.test

@@ -13,8 +13,6 @@ nextflow_process {
 
     test("align_sequence - compressed - seatoxin") {
 
-        config "./sequence.config"
-
         when {
             process {
                 """
@@ -39,8 +37,6 @@ nextflow_process {
 
     test("align_sequence - uncompressed - seatoxin") {
 
-        config "./sequence.config"
-
         when {
             process {
                 """
@@ -65,8 +61,6 @@ nextflow_process {
 
     test("align_with_guide_tree - uncompressed - seatoxin") {
 
-        config "./tree.config"
-
         setup {
 
             run("FAMSA_GUIDETREE") {
@@ -176,7 +170,6 @@ nextflow_process {
 
     test("align_sequence - uncompressed - seatoxin - stub") {
         options "-stub"
-        config "./sequence.config"
 
         when {
             process {

modules/nf-core/tcoffee/regressive/main.nf

@@ -21,18 +21,20 @@ process TCOFFEE_REGRESSIVE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args          = task.ext.args ?: ''
-    def prefix        = task.ext.prefix ?: "${meta.id}"
-    def tree_args     = tree ? "-reg_tree $tree" : ""
-    def template_args = template ? "-template_file $template" : ""
-    def outfile       = compress ? "stdout" : "${prefix}.aln"
+    def args               = task.ext.args ?: ''
+    def prefix             = task.ext.prefix ?: "${meta.id}"
+    def tree_args          = tree ? "-reg_tree $tree" : ""
+    def template_args      = template ? "-template_file $template" : ""
+    def default_out_format = ("-output" in "${args}") ? "" : "-output fasta_aln"
+    def outfile            = compress ? "stdout" : "${prefix}.aln"
     """
     export TEMP='./'
     t_coffee -reg \
         -seq ${fasta} \
         $tree_args \
         $template_args \
         $args \
+        $default_out_format \
         -reg_thread ${task.cpus} \
         -outfile $outfile
 

modules/nf-core/tcoffee/regressive/tests/main.nf.test

@@ -13,8 +13,6 @@ nextflow_process {
 
     test("align_sequence - compressed - seatoxin") {
 
-        config "./sequence.config"
-
         when {
             process {
                 """
@@ -39,8 +37,6 @@ nextflow_process {
 
     test("align_sequence - uncompressed - seatoxin") {
 
-        config "./sequence.config"
-
         when {
             process {
                 """
@@ -65,8 +61,6 @@ nextflow_process {
 
     test("align_with_guide_tree - uncompressed - seatoxin") {
 
-        config "./tree.config"
-
         setup {
 
             run("FAMSA_GUIDETREE") {
@@ -107,7 +101,6 @@ nextflow_process {
 
     test("align_sequence - uncompressed - seatoxin - stub") {
         options "-stub"
-        config "./sequence.config"
 
         when {
             process {

modules/nf-core/tcoffee/tcs/tests/lib.config

@@ -1,7 +1,7 @@
 process {
 
     withName: "TCOFFEE_ALIGN"{
-        ext.args = { "-output fasta_aln -out_lib sample_lib1.tc_lib" }
+        ext.args = { "-out_lib sample_lib1.tc_lib" }
     }
 
 }

subworkflows/nf-core/mafft_align/main.nf

@@ -0,0 +1,16 @@
+include { MAFFT_ALIGN as MAFFT_ALIGN_MODULE } from '../../../modules/nf-core/mafft/align/main'
+
+workflow MAFFT_ALIGN {
+
+    take:
+    ch_fasta // channel: [ val(meta), fasta ]
+
+    main:
+
+    MAFFT_ALIGN_MODULE ( ch_fasta, [[], []], [[], []], [[], []], [[], []], [[], []], [] )
+
+    emit:
+    // TODO nf-core: edit emitted channels
+    alignment = MAFFT_ALIGN_MODULE.out.fas      // channel: [ val(meta), *.fas ]
+    versions  = MAFFT_ALIGN_MODULE.out.versions // channel: [ versions.yml ]
+}

subworkflows/nf-core/mafft_align/meta.yml

@@ -0,0 +1,60 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "mafft_align"
+description: Prepare channels for running MAFFT/align
+keywords:
+  - msa
+  - mafft
+  - align
+components:
+  - mafft/align
+input:
+  - ch_fasta:
+      type: file
+      description: |
+        The input channel containing the FASTA files
+      pattern: "*.{bam/cram/sam}"
+      structure:
+        - - meta:
+              type: map
+              description: |
+                Groovy Map containing sample information
+                e.g. `[ id:'sample1', single_end:false ]`
+          - fasta:
+              type: file
+              description: Input sequences in FASTA format
+              pattern: "*.{fa,fasta}"
+              ontologies:
+                - edam: http://edamontology.org/format_1929
+output:
+  - alignment:
+      type: file
+      description: Channel containing the alignment file in fasta format.
+      structure:
+        - - meta:
+              type: map
+              description: |
+                Groovy Map containing sample information
+                e.g. `[ id:'test']`
+          - "*.aln.gz":
+              type: file
+              description: Alignment file, in FASTA format.
+              pattern: "*.aln.gz"
+              ontologies:
+                - edam: http://edamontology.org/format_1984
+  - versions:
+      type: file
+      description: Channel containing the software versions YAML file
+      structure:
+        - versions.yml:
+            type: file
+            description: File containing software versions
+            pattern: "versions.yml"
+            ontologies:
+              - edam: http://edamontology.org/format_3750 # YAML
+
+authors:
+  - "@mirpedrol"
+maintainers:
+  - "@mirpedrol"
+  - "@luisas"
+  - "@JoseEspinosa"

subworkflows/nf-core/mafft_align/tests/main.nf.test

@@ -0,0 +1,36 @@
+nextflow_workflow {
+
+    name "Test Subworkflow MAFFT_ALIGN"
+    script "../main.nf"
+    workflow "MAFFT_ALIGN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/mafft_align"
+    tag "mafft"
+    tag "mafft/align"
+
+
+    test("seatoxin-ref - fasta") {
+
+        when {
+            workflow {
+                """
+                input[0] = [
+                    [ [ id:'test' ] ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out
+                ).match() }
+            )
+        }
+    }
+
+}

subworkflows/nf-core/mafft_align/tests/main.nf.test.snap

@@ -0,0 +1,39 @@
+{
+    "seatoxin-ref - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            {
+                                "id": "test"
+                            }
+                        ],
+                        "[test].fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e84c35bc0c2b5e69b0e70e5063a04b00"
+                ],
+                "alignment": [
+                    [
+                        [
+                            {
+                                "id": "test"
+                            }
+                        ],
+                        "[test].fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e84c35bc0c2b5e69b0e70e5063a04b00"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-12-10T10:56:30.188643"
+    }
+}