Merge pull request #126 from lrauschning/mtmalign

add MTMalign

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -49,7 +49,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code

README.md

@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/multiplesequencealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -49,7 +49,7 @@ Available ALIGN methods:
 - MAGUS
 - MUSCLE5
 - MTMALIGN
-- TCOFFEE
+- T-COFFEE
 - 3DCOFFEE
 
 ## Usage

conf/modules.config

@@ -109,7 +109,8 @@ process {
         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|MTMALIGN_ALIGN"{
         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}" }

modules.json

@@ -65,6 +65,11 @@
                         "git_sha": "dc37bcdfa78fe3e9ca56e4b85e1621333c7b4301",
                         "installed_by": ["modules"]
                     },
+                    "mtmalign/align": {
+                        "branch": "master",
+                        "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",

modules/local/multiqc.nf

@@ -1,10 +1,8 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda 'bioconda::multiqc=1.21'
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+    conda 'bioconda::multiqc=1.22.1'
+    container "community.wave.seqera.io/library/pip_multiqc:2c2e276ad8997cc4"
 
     input:
     path multiqc_config

nextflow.config

@@ -257,7 +257,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/multiplesequencealign'
     description     = """Pipeline to run and benchmark multiple sequence alignment tools."""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.1'
     version         = '0.1.0dev'
     doi             = ''
 }

subworkflows/local/align.nf

@@ -16,6 +16,7 @@ include {   MUSCLE5_SUPER5                    } from '../../modules/nf-core/musc
 include {   TCOFFEE_ALIGN                     } from '../../modules/nf-core/tcoffee/align/main'
 include {   TCOFFEE_ALIGN as TCOFFEE3D_ALIGN  } from '../../modules/nf-core/tcoffee/align/main'
 include {   TCOFFEE_ALIGN as REGRESSIVE_ALIGN } from '../../modules/nf-core/tcoffee/align/main'
+include {   MTMALIGN_ALIGN                    } from '../../modules/nf-core/mtmalign/align/main'
 
 workflow ALIGN {
     take:
@@ -75,6 +76,7 @@ workflow ALIGN {
             mafft:               it[0]["aligner"] == "MAFFT"
             magus:               it[0]["aligner"] == "MAGUS"
             muscle5:             it[0]["aligner"] == "MUSCLE5"
+            mtmalign:            it[0]["aligner"] == "MTMALIGN"
             tcoffee:             it[0]["aligner"] == "TCOFFEE"
             tcoffee3d:           it[0]["aligner"] == "3DCOFFEE"
             regressive:          it[0]["aligner"] == "REGRESSIVE"
@@ -195,7 +197,23 @@ workflow ALIGN {
     msa = msa.mix(REGRESSIVE_ALIGN.out.alignment)
 
 
+    // -----------------  MTMALIGN  ------------------
+    // this call discards the fasta, tree and template arguments, as MTMalign only takes pdb inputs
+    // nonetheless, this is required by the pipeline
+    ch_pdb_mtmalign = ch_fasta_trees.mtmalign.map{ meta, fasta, tree -> [meta["id"], meta] }
+                                .combine(ch_structures.map{ meta, template, structures -> [meta["id"], structures]}, by: 0)
+                                .multiMap{
+                                            merging_id, meta, templatefile, structuresfiles ->
+                                                pdbs: [ meta, structuresfiles ]
+                                }
+
+    MTMALIGN_ALIGN(ch_pdb_mtmalign.pdbs, false)
+    ch_versions = ch_versions.mix(MTMALIGN_ALIGN.out.versions.first())
+    msa = msa.mix(MTMALIGN_ALIGN.out.alignment)
+
+
     emit:
     msa
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
+