Merge pull request #139 from luisas/foldmason

Foldmason

CHANGELOG.md

@@ -31,6 +31,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#89](https://github.com/nf-core/multiplesequencealign/issues/89)] - Add collection of plddt metrics in stats subworkflow.
 - [[#96](https://github.com/nf-core/multiplesequencealign/issues/96)] - Add collection of number of gaps in eval subworkflow.
 - [[#84](https://github.com/nf-core/multiplesequencealign/issues/84)] - Update Metromap
+- [[#139](https://github.com/nf-core/multiplesequencealign/pull/139)] - Add Foldmason
 
 ### `Fixed`
 

CITATIONS.md

@@ -22,6 +22,10 @@
 
 - [FAMSA](https://pubmed.ncbi.nlm.nih.gov/27670777/)
 
+  > Cameron Laurence Mathison Gilchrist, Milot Mirdita, Martin Steinegger: Multiple Protein Structure Alignment at Scale with FoldMason. bioRxiv 2024.08.01.606130; doi: https://doi.org/10.1101/2024.08.01.606130
+
+- [FoldMason](https://www.biorxiv.org/content/10.1101/2024.08.01.606130v3)
+
   > Deorowicz S, Debudaj-Grabysz A, Gudyś A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci Rep. 2016 Sep 27;6:33964. doi: 10.1038/srep33964. PMID: 27670777; PMCID: PMC5037421.
 
 - [Kalign3](https://pubmed.ncbi.nlm.nih.gov/31665271/)

conf/modules.config

@@ -108,7 +108,7 @@
             ext.prefix = { "${meta.id}" }
         }
 
-        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN"{
+        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|FOLDMASON_EASYMSA"{
             tag = { "${meta.id} tree:${meta.tree} argstree:${args_tree} args:${meta.args_aligner}" }
             ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
             ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }

docs/extending.md

@@ -24,15 +24,19 @@ The subworkflows are to a significant degree isolated from each other, and not a
 
 ## Adding an aligner
 
-1. Create a local or nf-core module and ensure the output is in FASTA format
-2. Add the aligner to the usage.md
-3. Add the aligner to the aligner config in `conf/modules.config`, see an example [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/conf/modules.config#L113). If required, also add other config options
-4. Include the module in the alignment subworkflow (`subworkflows/local/align.nf`)
-   - Import the module in the top, view an example [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/subworkflows/local/align.nf#L9)
-   - Add a branch to the alignment steps [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/subworkflows/local/align.nf#L73-L85)
-   - Call the aligner with the respective branch; you can either pass or discard a guidetree or structures using the multimap before the call step, see the CLUSTALO example [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/subworkflows/local/align.nf#L104-L113)
-   - Feed the output alignment and versions channels back into the `msa` the CLUSTALO example) and `ch_versions` channels (see the respective CLUSTALO example [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/subworkflows/local/align.nf#L113) and [here](https://github.com/nf-core/multiplesequencealign/blob/000ef2a535ed246ff89c7cd93afaca53879af3ef/subworkflows/local/align.nf#L112)). Make sure to `mix()` them so they do not get overwritten!
-
+-[] Create a module for your tool (ideally nf-core). Ensure the output is in FASTA format. Use other modules in the pipeline as template.
+-[] Include the module in the alignment subworkflow (`subworkflows/local/align.nf`)
+
+- Import the module
+- Add a branch to the correct channel, depending on your tool input (see other examples)
+- Call the aligner with the respective branch (see other examples)
+- Feed the output alignment and versions channels back into the `msa`. Make sure to `mix()` them so they do not get overwritten!
+  -[] Add the aligner to the aligner config in `conf/modules.config`.
+  -[] Update docs/usage.md
+  -[] Update CITATIONS.md
+  -[] Update CHANGELOG.md
+
+You can look at an example of a new tool integration [here](https://github.com/nf-core/multiplesequencealign/pull/139).
 Congratulations, your aligner is now in nf-core/multiplesequencalignment!
 
 ## Adding a guide tree estimator

docs/usage.md

@@ -58,6 +58,7 @@ The available ALIGN methods are listed below (those that accept guide trees are
 **STRUCTURE-BASED** (only require stuctures as input):
 
 - [MTMALIGN](https://bio.tools/mtm-align)
+- [FOLDMASON](https://github.com/steineggerlab/foldmason)
 
 ### 4. EVALUATE
 

modules.json

@@ -36,6 +36,11 @@
                         "git_sha": "e21abdefe46e27b71e0ced2cadc0f2463298aba6",
                         "installed_by": ["modules"]
                     },
+                    "foldmason/easymsa": {
+                        "branch": "master",
+                        "git_sha": "bea7a09bc85c756b8f2befd63311eb1651067073",
+                        "installed_by": ["modules"]
+                    },
                     "kalign/align": {
                         "branch": "master",
                         "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282",
@@ -68,7 +73,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "fe9614c5d1d9820dae56a5e30a07ba336db45835",
+                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
                     },
                     "muscle5/super5": {