Merge pull request #145 from luisas/add_consensus

Add consensus
nf-core · Sep 16, 2024 · da8af09 · da8af09
2 parents 37d2a1b + 0a17722
commit da8af09
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#84](https://github.com/nf-core/multiplesequencealign/issues/84)] - Update Metromap.
 - [[#139](https://github.com/nf-core/multiplesequencealign/pull/139)] - Add Foldmason.
 - [[#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.
 
 ### `Fixed`
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -122,8 +122,7 @@
         withName: "CREATE_TCOFFEETEMPLATE" {
             ext.prefix = { "${meta.id}" }
         }
-
-        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN|FOLDMASON_EASYMSA" {
+        withName: "CLUSTALO_ALIGN|FAMSA_ALIGN|FOLDMASON_EASYMSA|KALIGN_ALIGN|LEARNMSA_ALIGN|MAFFT|MAGUS_ALIGN|MUSCLE5_SUPER5|REGRESSIVE|TCOFFEE_ALIGN|TCOFFEE3D_ALIGN" {
             tag = {
                 [
                     "${meta.id}",
@@ -165,7 +164,13 @@
 
         }
 
-        withName:"PIGZ_COMPRESS" {
+        withName: 'CONSENSUS'{
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.args = { "-output fasta_aln" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        }
+
+        withName:"PIGZ_COMPRESS"{
             publishDir = [
                 path: { "${params.outdir}/alignment/${meta.id}" },
                 mode: params.publish_dir_mode,

diff --git a/docs/images/nf-core-msa_metro_map.png b/docs/images/nf-core-msa_metro_map.png
diff --git a/docs/usage.md b/docs/usage.md
@@ -60,6 +60,8 @@ The available ALIGN methods are listed below (those that accept guide trees are
 - [MTMALIGN](https://bio.tools/mtm-align)
 - [FOLDMASON](https://github.com/steineggerlab/foldmason)
 
+Optionally, [M-COFFEE](https://tcoffee.org/Projects/mcoffee/index.html) will combine the output of all alignments into a consensus MSA (--build_consensus).
+
 ### 4. EVALUATE
 
 Optionally, the produced MSAs can be evaluated. This step can be skipped using the `--skip_eval` parameter. The evaluations implemented are listed below.

diff --git a/modules.json b/modules.json
@@ -101,6 +101,11 @@
                         "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59",
                         "installed_by": ["modules"]
                     },
+                    "tcoffee/consensus": {
+                        "branch": "master",
+                        "git_sha": "8b8d8daa4b7d75ccfb290fcb721a00cc98e23567",
+                        "installed_by": ["modules"]
+                    },
                     "tcoffee/irmsd": {
                         "branch": "master",
                         "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59",

diff --git a/modules/nf-core/tcoffee/consensus/environment.yml b/modules/nf-core/tcoffee/consensus/environment.yml
diff --git a/modules/nf-core/tcoffee/consensus/main.nf b/modules/nf-core/tcoffee/consensus/main.nf
diff --git a/modules/nf-core/tcoffee/consensus/meta.yml b/modules/nf-core/tcoffee/consensus/meta.yml
diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test b/modules/nf-core/tcoffee/consensus/tests/main.nf.test
diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
diff --git a/modules/nf-core/tcoffee/consensus/tests/sequence.config b/modules/nf-core/tcoffee/consensus/tests/sequence.config