Merge pull request #3 from snakemake-workflows/refactor/all

refactor: all files are refactored

Author: cmeesters

workflow/Snakefile

@@ -3,97 +3,160 @@ from os import path
 
 from snakemake.utils import min_version
 
-min_version("7.19.1") # this is where SLURM support was introduced
+min_version("7.19.1")  # this is where SLURM support was introduced
 
-INPUT_DIR=config["INPUT_DIR"]
+INPUT_DIR = config["INPUT_DIR"]
 
-MIN_DIR=config["PREPARED_LIGAND_DIR"]
+MIN_DIR = config["PREPARED_LIGAND_DIR"]
 
-PREPARED_DIR=config["PREPARED_DATA_DIR"]
+PREPARED_DIR = config["PREPARED_DATA_DIR"]
 
-OUTPUT_DIR=config["OUTPUT_DIR"]
+OUTPUT_DIR = config["OUTPUT_DIR"]
 
-TMP_DIR=config["TEMP_DATA_DIR"]
+TMP_DIR = config["TEMP_DATA_DIR"]
 
-LOCAL_INPUT =config["LOCAL_INPUT_DIR"]
+LOCAL_INPUT = config["LOCAL_INPUT_DIR"]
 
 DATABASE = config["DATABASE"]
 
 SUBSET = config["SUBSET"]
 
 RESCREENING_TARGETS = config["RESCREENING_TARGETS"]
 
+
 def generateOutput(wildcards):
     irods = path.join(OUTPUT_DIR, "results", "irods.json")
     if config["RESCREENING"] == "TRUE":
-        out = expand(path.join(OUTPUT_DIR, "results", "rescreening_{percentage}", "{receptorID}", "union.csv"),
-            receptorID = config["TARGETS"][0].split(',')[0],
-            percentage = config["RESULT_NUMBER"],
-            combAll = combAll)
-        hist = expand(path.join(OUTPUT_DIR, "results", "{receptorID}_hist.png"),
-            receptorID = config["TARGETS"][0].split(',')[0])
+        out = expand(
+            path.join(
+                OUTPUT_DIR,
+                "results",
+                "rescreening_{percentage}",
+                "{receptorID}",
+                "union.csv",
+            ),
+            receptorID=config["TARGETS"][0].split(",")[0],
+            percentage=config["RESULT_NUMBER"],
+            combAll=combAll,
+        )
+        hist = expand(
+            path.join(OUTPUT_DIR, "results", "{receptorID}_hist.png"),
+            receptorID=config["TARGETS"][0].split(",")[0],
+        )
 
-        return hist + out  + [irods]
+        return hist + out + [irods]
 
     else:
-        out = expand(path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"),
-            receptorID = config["TARGETS"][0].split(',')[0],
-            percentage = config["RESULT_NUMBER"])
-        hist = expand(path.join(OUTPUT_DIR, "results", "{receptorID}_hist.png"),
-            receptorID = config["TARGETS"][0].split(',')[0])
+        out = expand(
+            path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"),
+            receptorID=config["TARGETS"][0].split(",")[0],
+            percentage=config["RESULT_NUMBER"],
+        )
+        hist = expand(
+            path.join(OUTPUT_DIR, "results", "{receptorID}_hist.png"),
+            receptorID=config["TARGETS"][0].split(",")[0],
+        )
         return hist + out + [irods]
 
 
-localrules: all, generateIRODS, dockingResultsTxt, removeDuplicateLigands, makeVenn, prepareLigands2, mergeDocking2, bestLigands, prepareSecondDocking, convertMol2, makeReceptorPDBQT, mergeDocking ,mergeLocalInput, split, split2, targetProtein, getZINCdata, getZINCSubsets, gunzip,  ENAMINEdownload, prepareReceptor, prepareDocking, prepareLibrary, prepareGeometry, makeHistogram, cleanLigands
-
-targetList=[]   #get ProteinIDs from configfile for rescreening
+localrules:
+    all,
+    generateIRODS,
+    dockingResultsTxt,
+    removeDuplicateLigands,
+    makeVenn,
+    prepareLigands2,
+    mergeDocking2,
+    bestLigands,
+    prepareSecondDocking,
+    convertMol2,
+    makeReceptorPDBQT,
+    mergeDocking,
+    mergeLocalInput,
+    split,
+    split2,
+    targetProtein,
+    getZINCdata,
+    getZINCSubsets,
+    gunzip,
+    ENAMINEdownload,
+    prepareReceptor,
+    prepareDocking,
+    prepareLibrary,
+    prepareGeometry,
+    makeHistogram,
+    cleanLigands,
+
+
+targetList = []  # get ProteinIDs from configfile for rescreening
 for i in config["RESCREENING_TARGETS"]:
-    targetList.append(i.split(',')[0])
+    targetList.append(i.split(",")[0])
 
 combList = []
 for comb in itertools.combinations(targetList, 2):  # all combinations of two targets
 
-    combList.append('_'.join(comb))
+    combList.append("_".join(comb))
+
+combAll = "_".join(targetList)  # combine all rescreening targets
 
-combAll = '_'.join(targetList) # combine all rescreening targets
 
 def getAllVenn(wildcards):
-    path.join(OUTPUT_DIR, "output", "rescreening", "{receptorID}", "{RESCREENING_TARGETS}_union.txt")
+    path.join(
+        OUTPUT_DIR,
+        "output",
+        "rescreening",
+        "{receptorID}",
+        "{RESCREENING_TARGETS}_union.txt",
+    )
 
 
 def IRODSinput(wildcards):
     if config["RESCREENING"] == "TRUE":
-        out = expand(path.join(OUTPUT_DIR, "results", "rescreening_{percentage}", "{receptorID}", "union.csv"),
-            receptorID = config["TARGETS"][0].split(',')[0],
-            percentage = config["RESULT_NUMBER"],
-            combAll = combAll)
+        out = expand(
+            path.join(
+                OUTPUT_DIR,
+                "results",
+                "rescreening_{percentage}",
+                "{receptorID}",
+                "union.csv",
+            ),
+            receptorID=config["TARGETS"][0].split(",")[0],
+            percentage=config["RESULT_NUMBER"],
+            combAll=combAll,
+        )
     else:
-        out = expand(path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"),
-            receptorID = config["TARGETS"][0].split(',')[0],
-            percentage = config["RESULT_NUMBER"])
+        out = expand(
+            path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"),
+            receptorID=config["TARGETS"][0].split(",")[0],
+            percentage=config["RESULT_NUMBER"],
+        )
     return out
 
+
 def resources(RULE_NAME):
     out_list = []
     for key in config[RULE_NAME]:
-        out_list.append(f'{key} = {config[RULE_NAME][key]}')
-    out_str = ',\n'.join(out_list)
+        out_list.append(f"{key} = {config[RULE_NAME][key]}")
+    out_str = ",\n".join(out_list)
     return out_str
 
+
 rule all:
     input:
-        generateOutput
+        generateOutput,
+
 
 rule generateIRODS:
     input:
-        IRODSinput
+        IRODSinput,
     output:
-        path.join(OUTPUT_DIR, "results", "irods.json")
+        path.join(OUTPUT_DIR, "results", "irods.json"),
     log:
-        "logs/generateIRODS.log"
+        "logs/generateIRODS.log",
     script:
         "scripts/generateIRODS.py"
 
+
 include: "rules/analyse.smk"
 include: "rules/docking.smk"
 include: "rules/preparation.smk"