feat: Adding somatic neoepitope preparation workflow

snappy_pipeline/workflows/somatic_neoepitope_prediction/Snakefile

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+# -*- coding: utf-8 -*-
+"""CUBI Pipeline tumor mutational burden step Snakefile"""
+
+import os
+
+from snappy_pipeline import expand_ref
+from snappy_pipeline.workflows.somatic_neoepitope_prediction import (
+    SomaticNeoepitopePredictionWorkflow,
+)
+
+__author__ = "Pham Gia Cuong"
+
+
+# Configuration ===============================================================
+
+
+configfile: "config.yaml"
+
+
+# Expand "$ref" JSON pointers in configuration (also works for YAML)
+config, lookup_paths, config_paths = expand_ref("config.yaml", config)
+
+# WorkflowImpl Object Setup ===================================================
+wf = SomaticNeoepitopePredictionWorkflow(workflow, config, lookup_paths, config_paths, os.getcwd())
+
+
+localrules:
+    # Linking files from work/ to output/ should be done locally
+    neoepitope_preparation_link_out_run,
+
+
+rule all:
+    input:
+        wf.get_result_files(),
+
+
+# Generic linking out ---------------------------------------------------------
+
+
+rule neoepitope_preparation_link_out_run:
+    input:
+        wf.get_input_files("link_out", "run"),
+    output:
+        wf.get_output_files("link_out", "run"),
+    run:
+        shell(wf.get_shell_cmd("link_out", "run", wildcards))
+
+
+rule neoepitope_preparation:
+    input:
+        **wf.get_input_files("neoepitope_preparation", "run"),
+    output:
+        **wf.get_output_files("neoepitope_preparation", "run"),
+    log:
+        **wf.get_log_file("neoepitope_preparation", "run"),
+    threads: wf.get_resource("neoepitope_preparation", "run", "threads")
+    resources:
+        time=wf.get_resource("neoepitope_preparation", "run", "time"),
+        memory=wf.get_resource("neoepitope_preparation", "run", "memory"),
+        partition=wf.get_resource("neoepitope_preparation", "run", "partition"),
+        tmpdir=wf.get_resource("neoepitope_preparation", "run", "tmpdir"),
+    wrapper:
+        wf.wrapper_path("pvactools/combining")