mirpedrol · mirpedrol · Jan 23, 2025 · Jan 23, 2025 · Jan 23, 2025 · Jan 24, 2025
diff --git a/README.md b/README.md
@@ -138,7 +138,7 @@ nextflow run nf-core/multiplesequencealign \
 
 <details>
   <summary> FAQ: Can I specify the arguments of the tools (tree and aligner)? </summary>
-  Yes, use the <code>--args_tree</code> and <code>--args_aligner</code> flags. More info: <a href="https://nf-co.re/multiplesequencealign/usage">usage</a> and <a href="https://nf-co.re/multiplesequencealign/parameters">parameters</a>.
+  Yes, use the <code>--args_guidetree</code> and <code>--args_aligner</code> flags. More info: <a href="https://nf-co.re/multiplesequencealign/usage">usage</a> and <a href="https://nf-co.re/multiplesequencealign/parameters">parameters</a>.
 </details>
 
 ### CASE 2: Multiple datasets, multiple tools.
@@ -191,12 +191,12 @@ Please check: <a href="https://nf-co.re/multiplesequencealign/usage/#samplesheet
 
 Each line defines a combination of guide tree and multiple sequence aligner to run with the respective arguments to be used.
 
-The only required field is `aligner`. The fields `tree`, `args_tree` and `args_aligner` are optional and can be left empty.
+The only required field is `aligner`. The fields `tree`, `args_guidetree` and `args_aligner` are optional and can be left empty.
 
 A minimal version:
 
 ```csv
-tree,args_tree,aligner,args_aligner
+tree,args_guidetree,aligner,args_aligner
 ,,FAMSA,
 ```
 
@@ -205,7 +205,7 @@ This will run the FAMSA aligner.
 A more complex one:
 
 ```csv
-tree,args_tree,aligner,args_aligner
+tree,args_guidetree,aligner,args_aligner,
 FAMSA, -gt upgma -medoidtree, FAMSA,
 , ,TCOFFEE,
 FAMSA,,REGRESSIVE,

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -119,11 +119,11 @@ custom_table_header_config:
       hidden: false
       namespace: "Alignment"
       scale: "Paired"
-    args_tree:
+    args_guidetree:
       description: "Arguments used to build the tree."
       hidden: true
       namespace: "Alignment"
-    args_tree_clean:
+    args_guidetree_clean:
       description: "Arguments used to build the tree."
       hidden: true
       namespace: "Alignment"
@@ -145,7 +145,7 @@ table_columns_placement:
   summary_stats:
     fasta: 90
     tree: 150
-    args_tree: 170
+    args_guidetree: 170
     aligner: 200
     args_aligner: 220
     n_sequences: 250

diff --git a/assets/schema_tools.json b/assets/schema_tools.json
@@ -7,46 +7,63 @@
     "items": {
         "type": "object",
         "properties": {
-            "tree": {
+            "guidetree": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "tree name cannot contain spaces and must be a string",
-                "meta": ["tree"],
+                "errorMessage": "tree name cannot contain spaces",
+                "meta": ["guidetree"],
+                "default": "",
+                "enum": [
+                    "clustalo_guidetree",
+                    "famsa_guidetree",
+                    "magus_guidetree"
+                ]
+            },
+            "args_guidetree": {
+                "type": "string",
+                "meta": ["args_guidetree"],
                 "default": ""
             },
-            "args_tree": {
+            "treealign": {
+                "type": "string",
+                "meta": ["treealign"],
+                "pattern": "^\\S+$",
+                "errorMessage": "align name must be provided and cannot contain spaces",
+                "default": "",
+                "enum":[
+                    "clustalo_align",
+                    "famsa_align",
+                    "magus_align",
+                    "tcoffee_align"
+                ]
+            },
+            "args_treealign": {
                 "type": "string",
-                "meta": ["args_tree"],
+                "meta": ["args_treealign"],
                 "default": ""
             },
-            "aligner": {
+            "alignment": {
                 "type": "string",
-                "meta": ["aligner"],
+                "meta": ["alignment"],
                 "pattern": "^\\S+$",
                 "enum": [
-                    "CLUSTALO",
-                    "FAMSA",
-                    "KALIGN",
-                    "LEARNMSA",
-                    "MAFFT",
-                    "MAGUS",
-                    "MUSCLE5",
-                    "TCOFFEE",
-                    "REGRESSIVE",
-                    "UPP",
-                    "3DCOFFEE",
-                    "MTMALIGN",
-                    "FOLDMASON"
+                    "clustalo_align",
+                    "famsa_align",
+                    "kalign_align",
+                    "learnmsa_align",
+                    "magus_align",
+                    "muscle5_super5",
+                    "tcoffee_align"
                 ],
-                "errorMessage": "align name must be provided, has to be a string, cannot contain spaces and must be one of: CLUSTALO, FAMSA, KALIGN, LEARNMSA, MAFFT, MAGUS, MUSCLES, TCOFFEE, REGRESSIVE, UPP, 3DCOFFE, MTMALIGN or FOLDMASON",
+                "errorMessage": "align name must be provided, has to be a string, cannot contain spaces and must be one of the valid options.",
                 "default": ""
             },
-            "args_aligner": {
+            "args_alignment": {
                 "type": "string",
-                "meta": ["args_aligner"],
+                "meta": ["args_alignment"],
                 "default": ""
             }
         },
-        "required": ["aligner"]
+        "oneOf": [{ "required": ["alignment"] }, { "required": ["guidetree", "treealign"] }]
     }
 }
diff --git a/assets/test_toolsheet.csv b/assets/test_toolsheet.csv
@@ -0,0 +1,10 @@
+guidetree,args_guidetree,treealign,args_treealign,alignment,args_alignment
+,,,,clustalo_align,
+,,,,famsa_align,
+,,,,kalign_align,
+,,,,learnmsa_align,
+,,,,magus_align,
+,,,,muscle5_super5,
+,,,,tcoffee_align,
+famsa_guidetree,-gt upgma -medoidtree,famsa_align,
+famsa_guidetree,,magus_align,
diff --git a/assets/toolsheet.csv b/assets/toolsheet.csv
@@ -1,3 +1,3 @@
-tree,args_tree,aligner,args_aligner
+tree,args_guidetree,aligner,args_aligner
 FAMSA,,FAMSA,
 ,,MAFFT,--dpparttree
diff --git a/bin/merge_scores.py b/bin/merge_scores.py
@@ -5,7 +5,7 @@
 import sys
 import pandas as pd
 
-merging_cols = ["id", "tree", "args_tree", "aligner", "args_aligner"]
+merging_cols = ["id", "tree", "args_guidetree", "aligner", "args_aligner"]
 scores_files = sys.argv[2:]
 outfile = sys.argv[1]
 

diff --git a/bin/shiny_app/shiny_app.py b/bin/shiny_app/shiny_app.py
@@ -28,12 +28,12 @@
 def merge_tree_args(row):
     if str(row["tree"]) == "DEFAULT":
         return "DEFAULT"
-    elif str(row["args_tree_clean"]) == "default":
-        return str(row["tree"]) + " (default)"
-    elif pd.isna(row["args_tree_clean"]):
-        return str(row["tree"]) + " (default)"
+    elif str(row["args_guidetree_clean"]) == "default":
+        return str(row["guidetree"]) + " (default)"
+    elif pd.isna(row["args_guidetree_clean"]):
+        return str(row["guidetree"]) + " (default)"
     else:
-        return str(row["tree"]) + " (" + str(row["args_tree"]) + ")"
+        return str(row["guidetree"]) + " (" + str(row["args_guidetree"]) + ")"
 
 inputfile["tree_args"] = inputfile.apply(merge_tree_args, axis=1)
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -64,18 +64,18 @@
         }
 
         //
-        // Tree building
+        // Tree building (guidetree)
         //
 
-        withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAFFT_GUIDETREE" {
+        withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAGUS_GUIDETREE" {
             tag = {
                 [
                     "${meta.id}",
-                    meta.args_tree ? "args: ${meta.args_tree_clean}" : ""
+                    meta.args_guidetree ? "args: ${meta.args_guidetree}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}" }
-            ext.args = { "${meta.args_tree}" == "null" ? '' : "${meta.args_tree}" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}" }
+            ext.args = { "${meta.args_guidetree}" == "null" ? '' : "${meta.args_guidetree}" }
             publishDir = [
                 path: { "${params.outdir}/trees/${meta.id}" },
                 mode: params.publish_dir_mode,
@@ -84,65 +84,42 @@
         }
 
         //
-        // alignments
+        // Alignment from a tree (treealign)
         //
 
-        withName: "CREATE_TEMPLATE" {
-            ext.prefix = { "${meta.id}" }
-        }
-        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_ALIGN|KALIGN_ALIGN|MAFFT_ALIGN|MAGUS_ALIGN|MUSCLE5_ALIGN|REGRESSIVE_ALIGN|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|UPP_ALIGN" {
+        withName: "NFCORE_MULTIPLESEQUENCEALIGN:MULTIPLESEQUENCEALIGN:MSA_TREEALIGN:CLUSTALO_ALIGN|FAMSA_ALIGN|MAGUS_ALIGN|TCOFFEE_ALIGN"{
             tag = {
                 [
                     "${meta.id}",
-                    meta.tree ? "tree: ${meta.tree}" : "",
-                    meta.args_tree ? "argstree: ${meta.args_tree}" : "",
-                    meta.args_aligner ? "args: ${meta.args_aligner_clean}" : ""
+                    meta.args_treealign ? "args: ${meta.args_treealign}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
-            ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
-            if (params.skip_compression || (params.skip_eval && !params.build_consensus)) {
-                publishDir = [
-                    path: { "${params.outdir}/alignments/${meta.id}" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
+            ext.prefix = { "${meta.id}_${meta.treealign}-args-${meta.args_treealign_clean}_${meta.guidetree}-args-${meta.args_guidetree_clean}" }
+            ext.args = { "${meta.args_treealign}" == "null" ? '' : "${meta.args_treealign}" }
+            publishDir = [
+                path: { "${params.outdir}/alignment/${meta.id}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
 
-        withName: "LEARNMSA_ALIGN" {
-            tag = {
-                [
-                    "${meta.id}",
-                    meta.tree ? "tree: ${meta.tree}" : "",
-                    meta.args_tree ? "argstree: ${meta.args_tree}" : "",
-                    meta.args_aligner ? "args: ${meta.args_aligner_clean}" : ""
-                ].join(' ').trim()
-            }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
-            ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
+        //
+        // alignments
+        //
 
-            if(params.skip_compression){
-                publishDir = [
-                    path: { "${params.outdir}/alignments/${meta.id}" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
+        withName: "CREATE_TEMPLATE" {
+            ext.prefix = { "${meta.id}" }
         }
 
-        withName: "PIGZ_COMPRESS_LEARNMSA"{
+        withName: "NFCORE_MULTIPLESEQUENCEALIGN:MULTIPLESEQUENCEALIGN:MSA_ALIGNMENT:CLUSTALO_ALIGN|FAMSA_ALIGN|LEARNMSA_ALIGN|KALIGN_ALIGN|MUSCLE5_SUPER5|MAGUS_ALIGN|TCOFFEE_ALIGN" {
             tag = {
                 [
                     "${meta.id}",
-                    meta.tree ? "tree: ${meta.tree}" : "",
-                    meta.args_tree ? "argstree: ${meta.args_tree}" : "",
-                    meta.args_aligner ? "args: ${meta.args_aligner}" : ""
+                    meta.args_aligner ? "args: ${meta.args_alignment_clean}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
-            ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
-
+            ext.prefix = { "${meta.id}_${meta.alignment}-args-${meta.args_alignment_clean}" }
+            ext.args = { "${meta.args_alignment}" == "null" ? '' : "${meta.args_alignment}" }
             publishDir = [
                 path: { "${params.outdir}/alignments/${meta.id}" },
                 mode: params.publish_dir_mode,
@@ -156,11 +133,11 @@
                 [
                     "${meta.id}",
                     meta.tree ? "tree: ${meta.tree}" : "",
-                    meta.args_tree ? "argstree: ${meta.args_tree}" : "",
+                    meta.args_guidetree ? "argstree: ${meta.args_guidetree}" : "",
                     meta.args_aligner ? "args: ${meta.args_aligner}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}" }
             ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
             if(params.skip_compression){
                 publishDir = [
@@ -215,21 +192,21 @@
         //
 
         withName: 'PARSE_IRMSD' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_irmsd" }
         }
 
         withName: 'TCOFFEE_ALNCOMPARE_SP' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_sp" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_sp" }
             ext.args = "-compare_mode sp"
         }
 
         withName: 'TCOFFEE_ALNCOMPARE_TC' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tc" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_tc" }
             ext.args = "-compare_mode tc"
         }
 
         withName: 'TCOFFEE_IRMSD' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_irmsd" }
             publishDir = [
                 path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1].toLowerCase()}" },
                 mode: params.publish_dir_mode,
@@ -239,7 +216,7 @@
         }
 
         withName: "CALC_GAPS" {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_gaps" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_gaps" }
         }
 
         withName: "CONCAT_IRMSD" {
@@ -263,7 +240,7 @@
         }
 
         withName: 'TCOFFEE_TCS' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tcs" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}_tcs" }
             publishDir = [
                 path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1].toLowerCase()}" },
                 mode: params.publish_dir_mode,
@@ -310,7 +287,7 @@
         // Visualization
         //
         withName: 'FOLDMASON_MSA2LDDTREPORT' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.prefix = { "${meta.id}_${meta.guidetree}-args-${meta.args_guidetree_clean}_${meta.alignment ?: meta.treealign}-args-${meta.args_alignment_clean ?: meta.args_treealign_clean}" }
             publishDir = [
                 path: { "${params.outdir}/reports/visualization" },
                 mode: params.publish_dir_mode,