Add upp

CHANGELOG.md

@@ -35,6 +35,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#146](https://github.com/nf-core/multiplesequencealign/pull/146)] - Only show additional process tags when they exists and use the same ubuntu version in all modules.
 - [[#145](https://github.com/nf-core/multiplesequencealign/pull/145)] - Add consensus MSA.
 - [[#147](https://github.com/nf-core/multiplesequencealign/pull/147)] - Add small testing profile + some fixes of the shiny app.
+- [[#148](https://github.com/nf-core/multiplesequencealign/pull/148)] - Add UPP module.
 
 ### `Fixed`
 

CITATIONS.md

@@ -56,6 +56,10 @@
 
   > Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042. PMID: 10964570.
 
+- [UPP](https://academic.oup.com/bioinformatics/article/39/1/btad007/6982552)
+
+  > Park M, Ivanovic S, Chu G, Shen C, Warnow T. UPP2: fast and accurate alignment of datasets with fragmentary sequences. Bioinformatics. 2023 Jan 1;39(1):btad007. doi: 10.1093/bioinformatics/btad007. PMID: 36625535; PMCID: PMC9846425.
+
 ## Python packages
 
 - [Biopython](https://pubmed.ncbi.nlm.nih.gov/19304878/)

conf/modules.config

@@ -122,7 +122,7 @@
         withName: "CREATE_TCOFFEETEMPLATE" {
             ext.prefix = { "${meta.id}" }
         }
-        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_EASYMSA|KALIGN_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN" {
+        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_EASYMSA|KALIGN_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|UPP_ALIGN" {
             tag = {
                 [
                     "${meta.id}",

docs/usage.md

@@ -50,6 +50,7 @@ The available ALIGN methods are listed below (those that accept guide trees are
 - [MAGUS](https://github.com/vlasmirnov/MAGUS) (accepts guide tree)
 - [MUSCLE5](https://drive5.com/muscle5/manual/)
 - [TCOFFEE](https://tcoffee.readthedocs.io/en/latest/index.html) (accepts guide tree)
+- [UPP](https://github.com/smirarab/sepp) (accepts guide tree)
 
 **SEQUENCE- and STRUCTURE-BASED** (require both fasta and structures as input):
 

modules.json

@@ -125,6 +125,11 @@
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
+                    },
+                    "upp/align": {
+                        "branch": "master",
+                        "git_sha": "3be751e610b332efd94c2e82ddab5b5c65cfe852",
+                        "installed_by": ["modules"]
                     }
                 }
             },