Add DiffDock cwl and yml files as well as docker images and python sc…

…ripts

cwl_adapters/diffdock.cwl

@@ -0,0 +1,144 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: DiffDock Diffusion based protein ligand docking
+
+doc: |-
+  DiffDock Diffusion based protein ligand docking
+
+baseCommand: ["bash", "diffdock_cmds.sh"]
+
+hints:
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/diffdock_cpu
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+      ${
+        var lst = [];
+        lst.push(inputs.protein_path);
+        lst.push(inputs.ligand_path);
+        lst.push(inputs.script_path);
+        return lst;
+      }
+
+inputs:
+
+  script_path:
+    type: File
+
+  protein_path:
+    type: File
+
+  ligand_path:
+    type: File
+
+  protein_ligand_inputs:
+    label: csv file of protein and ligand file paths
+    type: File
+    inputBinding:
+      prefix: --protein_ligand_csv
+
+  inference_steps:
+    label: number of reverse diffusion steps
+    type: int?
+    inputBinding:
+      prefix: --inference_steps
+    default: 20
+
+  samples_per_complex:
+    label: Number of sample poses to generate per complex
+    type: int?
+    inputBinding:
+      prefix: --samples_per_complex
+    default: 40
+
+  batch_size:
+    label: input batch size for neural net
+    type: int?
+    inputBinding:
+      prefix: --batch_size
+    default: 10
+
+  out_dir:
+    label: where output from diffdock is saved
+    type: string?
+    inputBinding:
+      prefix: --out_dir
+    default: results/
+
+  model_dir:
+    label: directory of DiffDock score model from paper
+    type: string?
+    inputBinding:
+      prefix: --model_dir
+    default:  /DiffDock/workdir/paper_score_model/
+
+  confidence_model_dir:
+    label: directory of DiffDock confidence model from paper
+    type: string?
+    inputBinding:
+      prefix: --confidence_model_dir
+    default:  /DiffDock/workdir/paper_confidence_model
+
+  output_files:
+    type: string?
+
+  execution_time:
+    type: string?
+
+outputs:
+
+  output_files:
+    type: Directory?
+    outputBinding:
+      glob: $(inputs.out_dir)
+
+  stdout:
+    type: File
+    outputBinding:
+      glob: stdout
+
+  stderr:
+    type: File
+    outputBinding:
+      glob: stderr
+
+  execution_time:
+    label: Time to run DiffDock
+    doc: |-
+      Time to run DiffDock
+    type: float
+    outputBinding:
+      glob: stderr
+      loadContents: true
+      outputEval: |
+        ${
+          // the time command outputs to stderr and not to stdout
+          // example output below, parse the float value of seconds (first item in line)
+          // 345.6
+          const lines = self[0].contents.split("\n");
+          for (var i = 0; i < lines.length; i++) {
+            const indices = lines[i].split(" ");
+            if (indices.length == 1) {
+              if (indices[0] != '') {
+                  const datum = parseFloat(indices[0]);
+                  return datum;
+              }
+            }
+          }
+        }
+
+stdout: stdout
+
+stderr: stderr
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/diffdock_gpu.cwl

@@ -0,0 +1,149 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: DiffDock Diffusion based protein ligand docking
+
+doc: |-
+  DiffDock Diffusion based protein ligand docking
+
+baseCommand: ["bash", "diffdock_cmds.sh"]
+
+hints:
+  cwltool:CUDARequirement:
+    cudaVersionMin: "11.7"
+    cudaComputeCapabilityMin: "3.0"
+    cudaDeviceCountMin: 0
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/diffdock_gpu
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+      ${
+        var lst = [];
+        lst.push(inputs.protein_path);
+        lst.push(inputs.ligand_path);
+        lst.push(inputs.script_path);
+        return lst;
+      }
+
+inputs:
+
+  script_path:
+    type: File
+
+  protein_path:
+    type: File
+
+  ligand_path:
+    type: File
+
+  protein_ligand_inputs:
+    label: csv file of protein and ligand file paths
+    type: File
+    inputBinding:
+      prefix: --protein_ligand_csv
+
+  inference_steps:
+    label: number of reverse diffusion steps
+    type: int?
+    inputBinding:
+      prefix: --inference_steps
+    default: 20
+
+  samples_per_complex:
+    label: Number of sample poses to generate per complex
+    type: int?
+    inputBinding:
+      prefix: --samples_per_complex
+    default: 40
+
+  batch_size:
+    label: input batch size for neural net
+    type: int?
+    inputBinding:
+      prefix: --batch_size
+    default: 10
+
+  out_dir:
+    label: where output from diffdock is saved
+    type: string?
+    inputBinding:
+      prefix: --out_dir
+    default: results/
+
+  model_dir:
+    label: directory of DiffDock score model from paper
+    type: string?
+    inputBinding:
+      prefix: --model_dir
+    default:  /DiffDock/workdir/paper_score_model/
+
+  confidence_model_dir:
+    label: directory of DiffDock confidence model from paper
+    type: string?
+    inputBinding:
+      prefix: --confidence_model_dir
+    default:  /DiffDock/workdir/paper_confidence_model
+
+  output_files:
+    type: string?
+
+  execution_time:
+    type: string?
+
+outputs:
+
+  output_files:
+    type: Directory?
+    outputBinding:
+      glob: $(inputs.out_dir)
+
+  stdout:
+    type: File
+    outputBinding:
+      glob: stdout
+
+  stderr:
+    type: File
+    outputBinding:
+      glob: stderr
+
+  execution_time:
+    label: Time to run DiffDock
+    doc: |-
+      Time to run DiffDock
+    type: float
+    outputBinding:
+      glob: stderr
+      loadContents: true
+      outputEval: |
+        ${
+          // the time command outputs to stderr and not to stdout
+          // example output below, parse the float value of seconds (first item in line)
+          // 345.6
+          const lines = self[0].contents.split("\n");
+          for (var i = 0; i < lines.length; i++) {
+            const indices = lines[i].split(" ");
+            if (indices.length == 1) {
+              if (indices[0] != '') {
+                  const datum = parseFloat(indices[0]);
+                  return datum;
+              }
+            }
+          }
+        }
+
+stdout: stdout
+
+stderr: stderr
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/diffdock_rank_poses.cwl

@@ -0,0 +1,66 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: DiffDock Diffusion pose ranking
+
+doc: |-
+  DiffDock Diffusion pose ranking
+
+baseCommand: ["python", "/rank_diffdock_poses.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/rank_diffdock_poses
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+   listing:
+     - entry: $(inputs.output_files_path)
+       writable: true # toil requires this to copy/access the files in folder
+
+inputs:
+
+  output_files_path:
+    type: Directory
+
+  top_n_confident:
+    type: float
+    inputBinding:
+      prefix: --top_n_confident
+    default: 10
+
+  top_percent_confidence:
+    type: float
+    inputBinding:
+      prefix: --top_percent_confidence
+    default: 33
+
+  output_poses:
+    type: string?
+
+
+outputs:
+
+  output_poses:
+    type:
+      type: array
+      items: File
+    outputBinding:
+      glob: "*ranked*.sdf"
+    format: edam:format_3814
+
+  stdout:
+    type: File
+    outputBinding:
+      glob: stdout
+
+stdout: stdout
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl