update

assets/toolsheet.csv

@@ -1,2 +1,2 @@
 tree,args_tree,aligner,args_aligner
-FAMSA,,FAMSA,
+FAMSA,,FOLDMASON,

modules.json

@@ -60,7 +60,8 @@
                         "git_sha": "8541ec46706d6610b032748fa51acf4b3094ced8",
                         "installed_by": [
                             "modules"
-                        ]
+                        ],
+                        "patch": "modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff"
                     },
                     "kalign/align": {
                         "branch": "master",

modules/local/foldmason_createdb.nf

@@ -3,8 +3,9 @@ process FOLDMASON_CREATEDB {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
-
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'oras://community.wave.seqera.io/library/foldmason:2.7bd21ed--a45f76ed12b391e6':
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
     input:
     tuple val(meta) , path(pdbs)
 

modules/local/foldmason_msa2lddtreport.nf

@@ -3,8 +3,9 @@ process FOLDMASON_MSA2LDDTREPORT {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
-
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'oras://community.wave.seqera.io/library/foldmason:2.7bd21ed--a45f76ed12b391e6':
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
     input:
     tuple val(meta)  , path(msa)
     tuple val(meta2) , path(db)

subworkflows/local/align.nf

@@ -121,7 +121,7 @@ workflow ALIGN {
             metadependency, template, dependency, metatree, metaalign ->
                 [ metadependency+metatree , metaalign, template, dependency ]
         }
-        .combine(trees, by: 0)
+        .join(trees, by: 0)
         .map {
             metratreeanddep, metaalign, template, dependency, tree ->
                 [ metratreeanddep+metaalign, tree, template, dependency ]
@@ -130,6 +130,8 @@ workflow ALIGN {
             foldmason: it[0]["aligner"] == "FOLDMASON"
         }
         .set { ch_optional_data_tools_tree }
+
+
 
     // ------------------------------------------------
     // Compute the alignments
@@ -369,12 +371,17 @@ workflow ALIGN {
         ch_versions = ch_versions.mix(FOLDMASON_EASYMSA.out.versions.first())
     }
 
+
+    ch_msa.view()
+
     // -----------------  CONSENSUS  ------------------
     if(params.build_consensus){
         ch_msa.map{ meta, msa -> [ meta["id"], msa]}
             .groupTuple()
             .map{ id_meta, msas -> [ ["id": id_meta, "tree":"", "args_tree":"", "args_tree_clean":null, "aligner":"CONSENSUS", "args_aligner":"", "args_aligner_clean":null ], msas ]}
             .set{ ch_msa_consensus }
+
+        ch_msa_consensus.view()
 
         CONSENSUS(ch_msa_consensus, [[:],[]], compress)
         ch_msa = ch_msa.mix(CONSENSUS.out.alignment)

subworkflows/local/visualization.nf

@@ -13,7 +13,6 @@ workflow VISUALIZATION {
     ch_versions     = Channel.empty()
     ch_html         = Channel.empty()
 
-
     // Merge the msa and tree 
     // split the msa meta to be able to merge with the tree meta
     ch_msa
@@ -29,7 +28,6 @@ workflow VISUALIZATION {
         .set { ch_msa_tree_data }
 
 
-    ch_optional_data.view()
     // 
     // FOLDMASON VISUALISATION
     //
@@ -38,7 +36,6 @@ workflow VISUALIZATION {
         ch_optional_data
     )
 
-
     ch_msa_tree_data
         .combine(FOLDMASON_CREATEDB.out.db, by:0)
         .multiMap{
@@ -51,13 +48,12 @@ workflow VISUALIZATION {
             ch_msa_db_tree
         }
 
-    ch_msa_db_tree.tree.view()
-
+    ch_msa_db_tree.msa.view()
     FOLDMASON_MSA2LDDTREPORT(
         ch_msa_db_tree.msa,
         ch_msa_db_tree.db,
         ch_msa_db_tree.pdbs,
-        ch_msa_db_tree.tree
+        [[:],[]]
     )
 
     ch_html = FOLDMASON_MSA2LDDTREPORT.out.html