add visualization

assets/toolsheet.csv

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

conf/modules.config

@@ -269,4 +269,16 @@
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
+
+        //
+        // Visualization
+        //
+        withName: 'FOLDMASON_MSA2LDDTREPORT' {
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            publishDir = [
+                path: { "${params.outdir}/visualization" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
     }

modules.json

@@ -166,7 +166,8 @@
                         "git_sha": "1f94c91de2b9e9c6b42fca53e823cada9a8b8465",
                         "installed_by": [
                             "modules"
-                        ]
+                        ],
+                        "patch": "modules/nf-core/tcoffee/extractfrompdb/tcoffee-extractfrompdb.diff"
                     },
                     "tcoffee/irmsd": {
                         "branch": "master",

modules/local/foldmason_createdb.nf

@@ -0,0 +1,45 @@
+process FOLDMASON_CREATEDB {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
+
+    input:
+    tuple val(meta) , path(pdbs)
+
+    output:
+    tuple val(meta), path("${prefix}*"), emit: db
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    foldmason createdb \\
+        ${pdbs} \\
+        ${prefix} \\
+        $args \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}

modules/local/foldmason_msa2lddtreport.nf

@@ -0,0 +1,51 @@
+process FOLDMASON_MSA2LDDTREPORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
+
+    input:
+    tuple val(meta)  , path(msa)
+    tuple val(meta2) , path(db)
+    tuple val(meta3) , path(pdbs)
+    tuple val(meta4) , path(tree)
+
+    output:
+    tuple val(meta), path("${prefix}.html"), emit: html
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def options_tree = tree ? "--guide-tree $tree" : ""
+    """
+    foldmason msa2lddtreport \\
+        ${meta.id} \\
+        ${msa} \\
+        ${prefix}.html \\
+        $args \\
+        ${options_tree} \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}

nextflow.config

@@ -64,6 +64,9 @@ params {
     skip_shiny                = false
     shiny_trace_mode          = "latest" // all, latest
 
+    // Visualisation options
+    skip_visualisation        = false
+
     // Config options
     config_profile_name        = null
     config_profile_description = null

nextflow_schema.json

@@ -209,6 +209,11 @@
                 "shiny_trace_mode": {
                     "type": "string",
                     "description": "variable containing the shiny_trace mode to be used."
+                },
+                "skip_visualisation": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-fast-forward",
+                    "description": "Skip the visualization generation."
                 }
             }
         },

subworkflows/local/align.nf

@@ -384,5 +384,6 @@ workflow ALIGN {
 
     emit:
     msa      = ch_msa      // channel: [ val(meta), path(msa) ]
+    trees    = trees       // channel: [ val(meta), path(tree) ]
     versions = ch_versions // channel: [ versions.yml ]
 }

subworkflows/local/preprocess_optionaldata.nf → subworkflows/local/preprocess.nf

@@ -1,6 +1,7 @@
 
 include { TCOFFEE_EXTRACTFROMPDB } from '../../modules/nf-core/tcoffee/extractfrompdb/main'
-workflow PREPROCESS_OPTIONALDATA {
+
+workflow PREPROCESS {
     take:
     ch_optional_data          //channel: [ meta, [file1, ] ]
 

subworkflows/local/visualization.nf

@@ -0,0 +1,69 @@
+include {FOLDMASON_CREATEDB         } from '../../modules/local/foldmason_createdb.nf'
+include {FOLDMASON_MSA2LDDTREPORT   } from '../../modules/local/foldmason_msa2lddtreport.nf'
+
+workflow VISUALIZATION {
+
+    take:
+    ch_msa           // channel: [ meta, /path/to/file.* ]
+    ch_trees         // channel: [ meta, /path/to/file.* ]
+    ch_optional_data // channel: [ meta, /path/to/file.* ]
+
+    main:
+
+    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
+        .map{
+            meta, file -> [meta.subMap(["id", "tree", "args_tree", "args_tree_clean"]), meta, file]
+        }
+        .join( ch_trees, by:0, remainder: true)
+        .filter { it.size() == 4 }
+        .map{
+            tree_meta, meta, msa, tree -> [meta.subMap(["id"]), meta, msa, tree]
+        }
+        .join( ch_optional_data, by:0)
+        .set { ch_msa_tree_data }
+
+
+    ch_optional_data.view()
+    // 
+    // FOLDMASON VISUALISATION
+    //
+
+    FOLDMASON_CREATEDB(
+        ch_optional_data
+    )
+
+
+    ch_msa_tree_data
+        .combine(FOLDMASON_CREATEDB.out.db, by:0)
+        .multiMap{
+            id, meta, msafile, treefile, pdb, dbfiles -> 
+            msa:  [meta, msafile]
+            db:   [id  , dbfiles]
+            pdbs: [id  , pdb]
+            tree: [meta, treefile == null ? [] : treefile]
+        }.set{
+            ch_msa_db_tree
+        }
+
+    ch_msa_db_tree.tree.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
+
+    emit:
+    html =  ch_html
+    versions = ch_versions
+
+}

workflows/multiplesequencealign.nf

@@ -22,7 +22,9 @@ include { STATS                  } from '../subworkflows/local/stats'
 include { ALIGN                  } from '../subworkflows/local/align'
 include { EVALUATE               } from '../subworkflows/local/evaluate'
 include { TEMPLATES              } from '../subworkflows/local/templates'
-include { PREPROCESS_OPTIONALDATA} from '../subworkflows/local/preprocess_optionaldata'
+include { PREPROCESS             } from '../subworkflows/local/preprocess'
+include { VISUALIZATION          } from '../subworkflows/local/visualization'
+
 
 //
 // MODULE: local modules
@@ -177,9 +179,9 @@ workflow MULTIPLESEQUENCEALIGN {
     ch_versions = ch_versions.mix(FASTAVALIDATOR.out.versions)
 
     if(!params.skip_preprocessing){
-        PREPROCESS_OPTIONALDATA(ch_optional_data)
-        ch_optional_data = PREPROCESS_OPTIONALDATA.out.preprocessed_optionaldata
-        ch_versions = ch_versions.mix(PREPROCESS_OPTIONALDATA.out.versions)
+        PREPROCESS(ch_optional_data)
+        ch_optional_data = PREPROCESS.out.preprocessed_optionaldata
+        ch_versions = ch_versions.mix(PREPROCESS.out.versions)
     }
 
 
@@ -259,6 +261,15 @@ workflow MULTIPLESEQUENCEALIGN {
         ch_versions = ch_versions.mix(PREPARE_SHINY.out.versions)
     }
 
+
+    if (!params.skip_visualisation) {
+        VISUALIZATION (
+            ALIGN.out.msa,
+            ALIGN.out.trees,
+            ch_optional_data
+        )
+    }
+
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",