Merge pull request #178 from luisas/add_mafft_guidetree

Add mafft guidetree

CHANGELOG.md

@@ -40,6 +40,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#148](https://github.com/nf-core/multiplesequencealign/pull/148)] - Add UPP module.
 - [[#150](https://github.com/nf-core/multiplesequencealign/pull/150)] - Update modules and readme for pre-release.
 - [[#174](https://github.com/nf-core/multiplesequencealign/issues/174)] - Add the chaining of proteinfold output to MSA input.
+- [[#177](https://github.com/nf-core/multiplesequencealign/pull/177)] - Add MAFFT guidetree.
 
 ### `Fixed`
 

conf/modules.config

@@ -67,7 +67,7 @@
         // Tree building
         //
 
-        withName: "FAMSA_GUIDETREE" {
+        withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE" {
             tag = {
                 [
                     "${meta.id}",
@@ -83,46 +83,14 @@
             ]
         }
 
-        withName: "CLUSTALO_GUIDETREE" {
-            tag = {
-                [
-                    "${meta.id}",
-                    meta.args_tree ? "args: ${meta.args_tree}" : ""
-                ].join(' ').trim()
-            }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}" }
-            ext.args   = { "${meta.args_tree}" == "null" ? '' : "${meta.args_tree}" }
-            publishDir = [
-                path: { "${params.outdir}/trees/${meta.id}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: "MAGUS_GUIDETREE" {
-            tag = {
-                [
-                    "${meta.id}",
-                    meta.args_tree ? "args: ${meta.args_tree}" : ""
-                ].join(' ').trim()
-            }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}" }
-            ext.args   = { "${meta.args_tree}" == "null" ? '' : "${meta.args_tree}" }
-            publishDir = [
-                path: { "${params.outdir}/trees/${meta.id}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
         //
         // Alignment
         //
 
         withName: "CREATE_TCOFFEETEMPLATE" {
             ext.prefix = { "${meta.id}" }
         }
-        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_EASYMSA|KALIGN_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|TCOFFEE_REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|UPP_ALIGN" {
+        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_EASYMSA|KALIGN_ALIGN|LEARNMSA_ALIGN|MAFFT_ALIGN|MAGUS_ALIGN|MUSCLE5_SUPER5|TCOFFEE_REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|UPP_ALIGN" {
             tag = {
                 [
                     "${meta.id}",

docs/usage.md

@@ -35,6 +35,7 @@ Currently available GUIDE TREE methods are: (Optional):
 
 - [CLUSTALO](http://clustal.org/omega/#Documentation)
 - [FAMSA](https://github.com/refresh-bio/FAMSA)
+- [MAFFT](https://mafft.cbrc.jp/alignment/server/index.html)
 
 ### 3. Align
 

modules.json

@@ -57,12 +57,17 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "magus/align": {
+                    "mafft/align": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "868cb0d7fc4862991fb7c2b4cd7289806cd53f81",
+                        "installed_by": ["modules"]
+                    },
+                    "mafft/guidetree": {
+                        "branch": "master",
+                        "git_sha": "968b494e20f439a9ed3d23c89274e6a4a625eb92",
                         "installed_by": ["modules"]
                     },
-                    "magus/guidetree": {
+                    "magus/align": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]