reports-update

assets/alphafold_template.html

@@ -570,6 +570,23 @@ <h3> Download </h3>
       })
     }
 
+    const loadModel_n = () => {
+      reps = Object.keys(state.representations);
+      if (reps.length) {
+        state.representations = {};
+      } else {
+        reps = [DEFAULT_REPRESENTATION];
+      }
+
+	    // Load PDB entry
+      return stage.loadFile( uri(state.model) ).then( (o) => {
+        state.modelObject = o;
+        reps.forEach( (r) => addModelRepresentation(r) );
+        stage.setSpin(state.spin);
+        o.autoView();
+        setLoading(0);
+      })
+    }
     // Representations ---------------------------------------------------------
 
     const toggleModelRepresentation = (rep) => {

bin/generat_plots_2.py

@@ -207,21 +207,29 @@ def generate_plots(msa_path, plddt_paths, name, out_dir):
 alphfold_template = open(args.html_template, "r").read()
 alphfold_template = alphfold_template.replace(f"*sample_name_here*", args.name)
 
+alphfold_template2 = open(args.html_template, "r").read()
+alphfold_template2 = alphfold_template2.replace(f"*sample_name_here*", args.name)
+
+
 i = 0
 for structure in structures:
     alphfold_template = alphfold_template.replace(f"*_data_ranked_{i}.pdb*", open(structure, "r").read().replace("\n", "\\n"))
+    alphfold_template2 = alphfold_template2.replace(f"*_data_ranked_{i}.pdb*", structure)
     i += 1
 
 if True:
     if not args.msa.endswith("NO_FILE"):
         with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}seq_coverage.png", "rb") as in_file:
             alphfold_template = alphfold_template.replace("seq_coverage.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")
+        alphfold_template2 = alphfold_template2.replace("seq_coverage.png", f"{args.name + ('_' if args.name else '')}seq_coverage.png")
     else:
         alphfold_template = alphfold_template.replace("seq_coverage.png","")
+        alphfold_template2 = alphfold_template2.replace("seq_coverage.png","")
 
     for i in range(0, len(args.plddt)):
         with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}coverage_LDDT_{i}.png", "rb") as in_file:
             alphfold_template = alphfold_template.replace(f"coverage_LDDT_{i}.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")
+        alphfold_template2 = alphfold_template2.replace(f"coverage_LDDT_{i}.png", f"{args.name + ('_' if args.name else '')}coverage_LDDT_{i}.png")
 
 
 """
@@ -235,3 +243,6 @@ def generate_plots(msa_path, plddt_paths, name, out_dir):
 """
 with open(f"{args.output_dir}/{args.name}_alphafold.html", "w") as out_file:
     out_file.write(alphfold_template)
+
+with open(f"{args.output_dir}/{args.name}_alphafold2.html", "w") as out_file:
+    out_file.write(alphfold_template2)

conf/dbs.config

@@ -54,5 +54,5 @@ params {
     esm2_t36_3B_UR50D_contact_regression = 'https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt'
 
     // Esmfold paths
-    esmfold_params_path                         = "${params.esmfold_db}/*"
+    //esmfold_params_path                         = "${params.esmfold_db}/*"
 }

conf/gadi.config

@@ -12,22 +12,28 @@
 
 
 if (params.use_gpu) { singularity.runOptions = '--nv' }
+
 singularity.cacheDir = "/g/data/if89/singularity_cache/"
 singularity.autoMounts = true
+
 params {
     mode            = 'alphafold2'
     alphafold2_mode = 'split_msa_prediction'
     input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
-    alphafold2_db   = '/g/data/if89/alphafold2/standard/'
+    alphafold2_db   = '/g/data/if89/protienfold_dbs/alphafold2_dbs/'
     use_dgxa100 = false
-    esmfold_params_path   = '/g/data/if89/esm-fold/checkpoints'
+    esmfold_params_path   = '/g/data/if89/protienfold_dbs/esmfold_dbs/checkpoints'
+    colabfold_db                = "/g/data/if89/protienfold_dbs/colabfold_dbs"
+    colabfold_server        = 'local'
+    colabfold_model_preset  = 'alphafold2_ptm'
+
 }
 
 process {
     storage = "gdata/if89+scratch/${params.project}+gdata/${params.project}"
 
     if (params.use_gpu) {
-        withName: 'RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2' {
+        withName: 'RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2|RUN_ESMFOLD' {
             if (params.use_dgxa100){
                 queue = "dgxa100"
                 cpus = 16    
@@ -39,9 +45,9 @@ process {
         }
     }
 
-    withName: 'RUN_ESMFOLD' {
-        queue = "copyq"
-        cpus = 1
-        time = 10.h
+    withName: 'MMSEQS_COLABFOLDSEARCH' {
+        memory = 300.GB 
+        time = 16.h   
     }
+
 }

nextflow.config

@@ -13,7 +13,6 @@ params {
     input                       = null
     mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold}
     use_gpu                     = false
-
     // Alphafold2 parameters
     alphafold2_mode             = "standard"
     max_template_date           = "2020-05-14"

nextflow_schema.json

@@ -29,7 +29,7 @@
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
-                "mode": {
+               "mode": {
                     "type": "string",
                     "default": "alphafold2",
                     "description": "Specifies the mode in which the pipeline will be run",
@@ -194,6 +194,27 @@
                 }
             }
         },
+        "gadi_config_options": {
+            "title": "Institutional config options",
+            "type": "object",
+            "fa_icon": "fas fa-university",
+            "description": "Configurations for running on GADI at NCI.",
+            "help_text": ".",
+            "properties": {
+                "use_dgxa100": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "If true uses the DGXA 100 GPU nodes",
+                    "fa_icon": "fas fa-battery-full"
+                },
+                "project": {
+                    "type": "string",
+                    "description": "Thge project code on GADI.",
+                    "default": "",
+                    "fa_icon": "fas fa-users-cog"
+                }
+            }
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",

tower.yml

@@ -5,3 +5,5 @@ reports:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"
   "*_alphafold.html":
     display: "Predected structures"
+  "*_alphafold2.html":
+    display: "Predected structures 2"

workflows/colabfold.nf

@@ -56,7 +56,7 @@ workflow COLABFOLD {
     Channel
         .fromSamplesheet("input")
         .set { ch_fasta }
-
+    ch_fasta.view()
     if (params.colabfold_server == 'webserver') {
         //
         // MODULE: Run colabfold
@@ -91,7 +91,7 @@ workflow COLABFOLD {
         //
         // MODULE: Run mmseqs
         //
-        if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
+        if (params.colabfold_model_preset != 'alphafold2_ptm') {
             MULTIFASTA_TO_CSV(
                 ch_fasta
             )

workflows/esmfold.nf

@@ -50,6 +50,7 @@ workflow ESMFOLD {
     //
     // Create input channel from input file provided through params.input
     //
+
     Channel
         .fromSamplesheet("input")
         .set { ch_fasta }