Update

generate_sag_yaml.py

@@ -46,9 +46,10 @@ content: []
 """
 
 # Params to remove from the interface defined in the workflow yaml
-def get_params_to_remove(pipeline):
+def get_params_to_remove(pipeline, input_path = "./", workFlowData = None):
     to_remove = list()
-    workflow = read_yaml("workflows/" + pipeline + "/" + pipeline + ".yaml")
+    #workflow = read_yaml(input_path+"workflows/" + pipeline + "/" + pipeline + ".yaml")
+    workflow = workFlowData
     if "params_equals" in workflow.keys():
         params_equals = workflow["params_equals"]
         for line in params_equals:
@@ -58,10 +59,13 @@ def get_params_to_remove(pipeline):
                 to_remove.append(line["param_B"])
     return to_remove
 
-def generate_tool(toolname, pipeline, step_name):
-    to_remove = get_params_to_remove(pipeline)
+def generate_tool(toolname, pipeline, step_name, input_path = "./", workFlowData = None):
+    
+    to_remove = get_params_to_remove(pipeline, input_path, workFlowData)
+
     template = yaml.load(tool_template, Loader=yaml.FullLoader)
-    tool = read_yaml("tools/" + toolname + "/" + toolname + ".yaml")
+    
+    tool = read_yaml(input_path + "tools/" + toolname + "/" + toolname + ".yaml")
 
     template["name"] = tool["id"]
     template["title"] = tool["name"]
@@ -122,8 +126,9 @@ def generate_tool(toolname, pipeline, step_name):
     return template
 
 
-def generate_workflow_params(pipeline):
-    workflow = read_yaml("workflows/" + pipeline + "/" + pipeline + ".yaml")
+def generate_workflow_params(pipeline, input_path = "./", workflowData = None):
+    #workflow = read_yaml(input_path+ "workflows/" + pipeline + "/" + pipeline + ".yaml")
+    workflow = workflowData
     template = yaml.load(tool_template, Loader=yaml.FullLoader)
     template["name"] = "global_params"
     template["title"] = "Global parameters :"
@@ -131,7 +136,7 @@ def generate_workflow_params(pipeline):
         template["content"].append(option)
 
     if "input" in workflow:
-        raw_input = read_yaml("raw_inputs/" + workflow["input"] + ".yaml")
+        raw_input = read_yaml(input_path + "raw_inputs/" + workflow["input"] + ".yaml")
         for option in raw_input["options"]:
             template["content"].append(option)
 
@@ -142,12 +147,13 @@ def generate_workflow_params(pipeline):
     return template
 
 
-def generate_sag_yaml(pipeline, template, outdir):
+def generate_sag_yaml(pipeline, template, outdir, input_path = "./"):
     # reading template
     template = yaml.load(template, Loader=yaml.FullLoader)
-    config = read_yaml("workflows/" + pipeline + "/" + pipeline + ".yaml")
+    #config = read_yaml(input_path + 'workflows/' + pipeline + "/" + pipeline + ".yaml")
+    config = read_yaml(outdir + pipeline + "/" + pipeline + ".yaml")
 
-    template["App"]["project"] = outdir
+    template["App"]["project"] = outdir + pipeline + "/sagApp/"
     template["App"]["general"]["title"] = config["name"]
 
     # adding global parameters
@@ -159,7 +165,7 @@ def generate_sag_yaml(pipeline, template, outdir):
     )
     # predefined boxes
 
-    template["App"]["pages"][0]["boxes"].append(generate_workflow_params(pipeline))
+    template["App"]["pages"][0]["boxes"].append(generate_workflow_params(pipeline, input_path, config))
 
     page_number = 1
 
@@ -181,13 +187,28 @@ def generate_sag_yaml(pipeline, template, outdir):
         # for each tool in a step, create a box
         for tool in step["tools"]:
             # predefined boxes
-            template["App"]["pages"][page_number]["boxes"].append(generate_tool(tool,pipeline,step["name"]))
+            template["App"]["pages"][page_number]["boxes"].append(generate_tool(tool,pipeline,step["name"], input_path, config))
         page_number += 1
 
     return template
 
 
+def main():
+
+    if len(sys.argv) == 2:
+        # generate
+        data = generate_sag_yaml(sys.argv[1], app_template, sys.argv[2])
+        write_yaml("workflows/" + sys.argv[1] + "/sag.yaml", data)
+
+    elif len(sys.argv) > 2:
+        # generate
+        data = generate_sag_yaml(sys.argv[1], app_template, sys.argv[2], sys.argv[3])
+        write_yaml(sys.argv[2] + sys.argv[1] + "/sag.yaml", data)
+
+    else:
+        exit("""Needs 2 argument minimum; """);
+
+
+if __name__ == "__main__":
+    main()
 
-# generate
-data = generate_sag_yaml(sys.argv[1], app_template, sys.argv[2])
-write_yaml("workflows/" + sys.argv[1] + "/sag.yaml", data)

generate_workflow.py

@@ -20,10 +20,10 @@ STEPS = collections.OrderedDict()
 TOOLS = list()
 
 # Import all yaml files (workflow and tools)
-def import_yaml_files(workflow_name):
+def import_yaml_files(workflow_name, output_path = "./workflows/", input_path = "./"):
     # Import workflow yaml
     global WORKFLOW_YAML
-    WORKFLOW_YAML = read_yaml("workflows/" + workflow_name + "/" + workflow_name + ".yaml")
+    WORKFLOW_YAML = read_yaml(output_path + workflow_name + "/" + workflow_name + ".yaml")
     
     # Import steps
     global STEPS
@@ -39,13 +39,13 @@ def import_yaml_files(workflow_name):
         global TOOLS_YAML
         for tool in step["tools"]:
             TOOLS.append(tool)
-            TOOLS_YAML[tool] = read_yaml("tools/" + tool + "/" + tool + ".yaml")
+            TOOLS_YAML[tool] = read_yaml(input_path + "tools/" + tool + "/" + tool + ".yaml")
     
     # Import base yaml (versions and citations for base container)
     global BASE_CITATIONS_YAML
-    BASE_CITATIONS_YAML = read_yaml("Docker_base/citations.yaml")
+    BASE_CITATIONS_YAML = read_yaml(input_path+"Docker_base/citations.yaml")
     global BASE_VERSIONS_YAML
-    BASE_VERSIONS_YAML = read_yaml("Docker_base/versions.yaml")
+    BASE_VERSIONS_YAML = read_yaml(input_path+"Docker_base/versions.yaml")
 
 def get_params_to_remove():
     # Get params to remove
@@ -60,7 +60,7 @@ def get_params_to_remove():
     return to_remove
 
 # Generate tool parameters with default values
-def generate_tool_params(workflow_name, to_remove):
+def generate_tool_params(workflow_name, to_remove, input_path = "./"):
     TOOL_PARAMS = collections.OrderedDict()
 
     # Global workflow parameters
@@ -71,7 +71,7 @@ def generate_tool_params(workflow_name, to_remove):
 
     # input parameters
     if "input" in WORKFLOW_YAML:
-        raw_inputs_yaml = read_yaml("./raw_inputs/" + WORKFLOW_YAML["input"] + ".yaml")
+        raw_inputs_yaml = read_yaml(input_path+"raw_inputs/" + WORKFLOW_YAML["input"] + ".yaml")
         for option in raw_inputs_yaml["options"]:
             TOOL_PARAMS[option["name"]] = option["value"] if ("value" in option.keys()) else ""
 
@@ -96,7 +96,7 @@ def generate_tool_params(workflow_name, to_remove):
     return TOOL_PARAMS
 
 # Generate parameters info (usefull for shiny app)
-def generate_params_info(to_remove):
+def generate_params_info(to_remove, input_path = "./"):
     PARAMS_INFO = collections.OrderedDict()
 
     for option in WORKFLOW_YAML["options"]:
@@ -108,7 +108,7 @@ def generate_params_info(to_remove):
 
     # input parameters
     if "input" in WORKFLOW_YAML:
-        raw_inputs_yaml = read_yaml("./raw_inputs/" + WORKFLOW_YAML["input"] + ".yaml")
+        raw_inputs_yaml = read_yaml(input_path+"raw_inputs/" + WORKFLOW_YAML["input"] + ".yaml")
         for option in raw_inputs_yaml["options"]:
             PARAMS_INFO[option["name"]] = collections.OrderedDict()
             PARAMS_INFO[option["name"]]["type"] = option["type"]
@@ -227,10 +227,10 @@ def generate_prepare_report_outputs():
 
     return PREPARE_REPORT_OUTPUTS
 
-def generate_snake_rule(step_name,tool_name):
+def generate_snake_rule(step_name,tool_name, input_path = "./"):
     RULE = "\n"
     
-    with open("tools/" + tool_name + "/" + tool_name + ".rule.snakefile", "r") as rule:
+    with open(input_path + "tools/" + tool_name + "/" + tool_name + ".rule.snakefile", "r") as rule:
         RULE += rule.read()
 
     RULE += "\n"
@@ -240,7 +240,7 @@ def generate_snake_rule(step_name,tool_name):
     return RULE
 
 # Generate Snakefile
-def generate_snakefile(workflow_name):
+def generate_snakefile(workflow_name, input_path = "./", output_path = "./workflows/"):
     SNAKEFILE = ""
     RULES = ""
 
@@ -255,27 +255,27 @@ def generate_snakefile(workflow_name):
     SNAKEFILE += "workdir: config['params']['results_dir']\n"
 
     # Open template
-    with open("workflows/" + workflow_name + "/" + workflow_name + ".snakefile", "r") as template:
+    with open(output_path + workflow_name + "/" + workflow_name + ".snakefile", "r") as template:
         SNAKEFILE += template.read()
 
     # import wildcards and imports
-    with open("workflows/global_imports.py", "r") as imports:
+    with open(input_path + "workflows/global_imports.py", "r") as imports:
         GLOBAL_IMPORTS = imports.read()
         SNAKEFILE = SNAKEFILE.replace("{import global_imports}",GLOBAL_IMPORTS)
 
     # Global functions
-    with open("workflows/global_functions.py") as global_functions:
+    with open(input_path + "workflows/global_functions.py") as global_functions:
         GLOBAL_FUNCTIONS = global_functions.read()
         SNAKEFILE = SNAKEFILE.replace("{import global_functions}",GLOBAL_FUNCTIONS)
 
     # Global rules
-    with open("workflows/global_rules.snakefile") as global_rules:
+    with open(input_path + "workflows/global_rules.snakefile") as global_rules:
         GLOBAL_RULES = global_rules.read()
         SNAKEFILE = SNAKEFILE.replace("{import global_rules}",GLOBAL_RULES)
     
     for step_name, step_yaml in STEPS.items():
         for tool in step_yaml["tools"]:
-            RULES += generate_snake_rule(step_name,tool)
+            RULES += generate_snake_rule(step_name,tool,input_path)
 
     SNAKEFILE = SNAKEFILE.replace("{import rules}", RULES)
     
@@ -290,10 +290,10 @@ def generate_snakefile(workflow_name):
     return SNAKEFILE
 
 # Generate Dockerfile
-def generate_dockerfile(workflow_name, output_dir, local_config):
+def generate_dockerfile(workflow_name, output_dir, local_config, input_file = "./"):
     DOCKERFILE = ""
     # Open template
-    with open("Dockerfile.template", "r") as template:
+    with open(input_file+"Dockerfile.template", "r") as template:
         DOCKERFILE = template.read()
     DOCKERFILE += "\n"
 
@@ -301,10 +301,10 @@ def generate_dockerfile(workflow_name, output_dir, local_config):
     files = ""
     if "data" in WORKFLOW_YAML.keys():
         for data in WORKFLOW_YAML["data"]:
-            file = "./workflows/" + workflow_name + "/data/" + data["name"]
-            files += "COPY ./files/data/" + data["name"] + " /" + data["name"] + "\n"
+            file = input_file + "workflows/" + workflow_name + "/data/" + data["name"]
+            files += "COPY " + output_dir+workflow_name +"/files/data/" + data["name"] + " /" + data["name"] + "\n"
             # Copy files
-            copy_dir(file,output_dir+'/files/data/'+data["name"])
+            copy_dir(file,output_dir+workflow_name+'/files/data/'+data["name"])
 
     # COPY files if data in tools yaml
     # And import install commands
@@ -313,10 +313,10 @@ def generate_dockerfile(workflow_name, output_dir, local_config):
         tools_installs.update(tool_yaml["install"])
         if "data" in tool_yaml.keys():
             for data in tool_yaml["data"]:
-                file = "./tools/" + tool_name + "/data/" + data["name"]
-                files += "COPY ./files/data/" + data["name"] + " /" + data["name"] + "\n"
+                file = input_file + "tools/" + tool_name + "/data/" + data["name"]
+                files += "COPY " + output_dir+workflow_name + "/files/data/" + data["name"] + " /" + data["name"] + "\n"
                 # Copy files
-                shutil.copytree(file, output_dir + '/files/data/' + data["name"])
+                shutil.copytree(file, output_dir+workflow_name + '/files/data/' + data["name"])
 
     files += "COPY files /workflow\n"
     files += "COPY sagApp /sagApp\n\n"
@@ -358,13 +358,13 @@ def generate_dockerfile(workflow_name, output_dir, local_config):
     return DOCKERFILE
 
 # Generate params yaml with all parameters and informations
-def generate_params_yaml(workflow_name, to_remove):
+def generate_params_yaml(workflow_name, to_remove, input_path = "./"):
     PARAMS = collections.OrderedDict()
 
     PARAMS["pipeline"] = workflow_name
-    PARAMS["params"] = generate_tool_params(workflow_name,to_remove)
+    PARAMS["params"] = generate_tool_params(workflow_name,to_remove, input_path)
     PARAMS["steps"] = list(STEPS.values())
-    PARAMS["params_info"] = generate_params_info(to_remove)
+    PARAMS["params_info"] = generate_params_info(to_remove, input_path)
     PARAMS["prepare_report_scripts"] = list(generate_prepare_report_scripts()["SCRIPTS"])
     PARAMS["prepare_report_outputs"] = generate_prepare_report_outputs()
     PARAMS["outputs"] = generate_outputs()
@@ -373,37 +373,37 @@ def generate_params_yaml(workflow_name, to_remove):
 
     return PARAMS
 
-def generate_pipeline_files(workflow_name, output_dir, local_config="default"):
+def generate_pipeline_files(workflow_name, output_dir, local_config="default", input_path = "./"):
     # Create output directory if needed
-    if not os.path.isdir(output_dir):
-        os.mkdir(output_dir)
-    if not os.path.isdir(output_dir+"/files"):
-        os.mkdir(output_dir+"/files")
+    if not os.path.isdir(output_dir + workflow_name):
+        os.mkdir(output_dir+workflow_name)
+    if not os.path.isdir(output_dir+workflow_name+"/files"):
+        os.mkdir(output_dir+workflow_name+"/files")
 
     ### Import yaml files and generate all output files
-    import_yaml_files(workflow_name)
+    import_yaml_files(workflow_name, output_dir, input_path)
 
-    write_yaml(output_dir + "/files/citations.yaml", generate_citations(workflow_name, output_dir))
+    write_yaml(output_dir+workflow_name + "/files/citations.yaml", generate_citations(workflow_name, output_dir))
 
-    write_yaml(output_dir + "/files/versions.yaml", generate_versions(workflow_name, output_dir))
+    write_yaml(output_dir+workflow_name + "/files/versions.yaml", generate_versions(workflow_name, output_dir))
     
-    with open(output_dir + "/files/Snakefile", "w") as out:
-        out.write(generate_snakefile(workflow_name))
+    with open(output_dir+workflow_name + "/files/Snakefile", "w") as out:
+        out.write(generate_snakefile(workflow_name, input_path, output_dir))
 
-    with open(output_dir + "/Dockerfile", "w") as out:
-        out.write(generate_dockerfile(workflow_name, output_dir, local_config))
+    with open(output_dir+workflow_name + "/Dockerfile", "w") as out:
+        out.write(generate_dockerfile(workflow_name, output_dir, local_config, input_path))
 
-    write_yaml(output_dir + "/files/params.total.yml", generate_params_yaml(workflow_name, get_params_to_remove()))
-    ###
+    write_yaml(output_dir+workflow_name + "/files/params.total.yml", generate_params_yaml(workflow_name, get_params_to_remove(), input_path))
+    ###1
 
     ### Copy scripts and other files
 
     NB_SCRIPTS = len(list(generate_prepare_report_scripts()["SCRIPTS"])) + len(list(generate_tools_scripts()))
 
-    if not os.path.isdir(output_dir + "/files/scripts"):
-        os.mkdir(output_dir + "/files/scripts")
+    if not os.path.isdir(output_dir+workflow_name + "/files/scripts"):
+        os.mkdir(output_dir+workflow_name + "/files/scripts")
     if (NB_SCRIPTS==0):
-        with open(output_dir + "/files/scripts/.gitignore",'w') as gitignore:
+        with open(output_dir+workflow_name + "/files/scripts/.gitignore",'w') as gitignore:
             to_write ="""# gitignore to force creation of scripts dir
 !.gitignore
 """
@@ -415,18 +415,18 @@ def generate_pipeline_files(workflow_name, output_dir, local_config="default"):
                 tool = script_dict["tool"]
                 script = script_dict["script"]
                 step = script_dict["step"]
-                returned_value = subprocess.call("sed 's/<step_name>/"+step+"/g' ./tools/" + tool + "/" + script + " > " + output_dir + "/files/scripts/" + step + "__" + script, shell=True)
+                returned_value = subprocess.call("sed 's/<step_name>/"+step+"/g' " + input_path + "tools/" + tool + "/" + script + " > " + output_dir + "/files/scripts/" + step + "__" + script, shell=True)
                 # search and replace <step_name>
                 #shutil.copy("./tools/" + tool + "/" + script, output_dir + "/files/scripts")
 
         for tool, script in generate_tools_scripts().items():
-            shutil.copy("./tools/" + tool + "/" + script, output_dir + "/files/scripts")    
+            shutil.copy(input_path+"tools/" + tool + "/" + script, output_dir +workflow_name+ "/files/scripts")    
 
-    shutil.copy("./generate_multiqc_config.py", output_dir + "/files")
-    shutil.copy("./tools.py", output_dir + "/files")
+    shutil.copy(input_path+"generate_multiqc_config.py", output_dir +workflow_name+ "/files")
+    shutil.copy(input_path+"tools.py", output_dir+workflow_name + "/files")
 
     if "input" in WORKFLOW_YAML:
-        shutil.copy("./raw_inputs/"+WORKFLOW_YAML["input"]+".py", output_dir+"/files")
+        shutil.copy(input_path+"raw_inputs/"+WORKFLOW_YAML["input"]+".py", output_dir+workflow_name+"/files")
 
     if (local_config != "default"):
         local_config_data = read_yaml(local_config)
@@ -435,8 +435,8 @@ def generate_pipeline_files(workflow_name, output_dir, local_config="default"):
                 qsub_file.writelines([ a.replace("{workflow_name}",WORKFLOW_YAML["docker_name"]) +'\n' for a in local_config_data["qsub"]] )
 
     # deploys scripts
-    for script in os.listdir("deploys"):
-        with open("deploys/"+script,"r") as infile:
+    for script in os.listdir(input_path+"deploys"):
+        with open(input_path+"deploys/"+script,"r") as infile:
             lines = infile.readlines()
             with open(output_dir+"/"+script,"w") as outfile:
                 outfile.writelines([ a.replace("{workflow_name}",WORKFLOW_YAML["docker_name"]) for a in lines] )
@@ -445,7 +445,9 @@ def generate_pipeline_files(workflow_name, output_dir, local_config="default"):
     ###
 
 def main():
-    if len(sys.argv) > 3:
+    if len(sys.argv) == 5:
+        generate_pipeline_files(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4])
+    elif len(sys.argv) > 3:
         generate_pipeline_files(sys.argv[1], sys.argv[2], sys.argv[3])
     elif len(sys.argv) == 3:
         generate_pipeline_files(sys.argv[1], sys.argv[2])

generate_workflow_snakefile.py

@@ -6,15 +6,26 @@
 
 from tools import read_yaml
 import sys
+import tempfile
+import shutil
+import os
 
-PATH_OUTPUT = "./"
-PATH_INPUT = "./workflows/"
+dirpath = tempfile.mkdtemp()
 
-def generate(name):
+DEFAULT_PATH_OUTPUT = "./"
+DEFAULT_PATH_INPUT = "./workflows/"
+
+def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output = DEFAULT_PATH_OUTPUT):
 
     result = "# File generate with generate_workflow_snakefile.py\n\n"
 
-    yaml = read_yaml(PATH_INPUT+name+"/"+name+".yaml")
+    yaml = None
+
+    if(path_yaml == ""):
+        yaml = read_yaml(path_input+name+"/"+name+".yaml")
+    else:
+        #print(path_yaml)
+        yaml = read_yaml(path_yaml)
 
     # imports
 
@@ -29,7 +40,7 @@ def generate(name):
     result += "\n"
 
     if "input" in yaml:
-        raw_inputs_yaml = read_yaml("./raw_inputs/"+yaml["input"]+".yaml")
+        raw_inputs_yaml = read_yaml(path_input+"/raw_inputs/"+yaml["input"]+".yaml")
         result += "# raw_inputs function call\n"
         result += yaml["input"]+" = "+raw_inputs_yaml["function_call"]+"\n"
         result += "config.update("+yaml["input"]+")\n"
@@ -136,20 +147,40 @@ def generate(name):
 
     #print(result)
 
-    
-
-    path_snakefile = PATH_INPUT + "/" + name + "/" + name + ".snakefile"
+    path_snakefile = path_output + name + "/" + name + ".snakefile"
+    #print(path_snakefile)
     f = open(path_snakefile, "w")
     f.write(result)
     f.close()
 
 
+def create_directory(output_path):
+
+    access_rights = 0o755
+
+    try:
+        os.mkdir(output_path, access_rights)
+    except OSError:
+        print ("Creation of the directory %s failed" % output_path)
+
+
 
 def main():
+
     if len(sys.argv) == 2:
         generate(sys.argv[1])
+
+    elif len(sys.argv) > 2:
+
+        name = sys.argv[1]
+        output_path = sys.argv[2]
+        path_yaml = output_path + name + "/" + name + ".yaml"
+        input_path = sys.argv[3]
+        
+        generate(name, path_yaml, input_path, output_path)
+
     else:
-        exit("""Needs 1 argument: workflow_name
+        exit("""Needs 1 argument minimum: workflow_name
 Usage: ./generate_workflow_snakefile.py workflow_name """)
 
 

output/.gitignore

+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

tools.py

@@ -3,7 +3,7 @@ import shutil
 
 def read_yaml(filepath):
     try:
-        with open(filepath, 'r') as file:
+        with open(filepath, 'rb') as file:
             data = yaml.load(file, Loader=yaml.FullLoader)
             return data
     except IOError as e:

tools/Picard_MarkDuplicates/Picard_MarkDuplicates.yaml

@@ -74,7 +74,7 @@
       "Picard Toolkit. 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute"
     ],
     samtools: [
-      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
+      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
     ]
   }
 }

tools/bcftools_mpileup/bcftools_mpileup.yaml

@@ -79,10 +79,10 @@
     },
   citations:  {
     bcftools: [
-      "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987–2993, https://doi.org/10.1093/bioinformatics/btr509"
+      "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https://doi.org/10.1093/bioinformatics/btr509"
     ],
     tabix: [
-      "Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, https://doi.org/10.1093/bioinformatics/btq671"
+      "Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718-719, https://doi.org/10.1093/bioinformatics/btq671"
     ]
   }
 }

tools/bowtie/bowtie.yaml

@@ -194,7 +194,7 @@
       "Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https://doi.org/10.1186/gb-2009-10-3-r25"
     ],
     samtools: [
-      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
+      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
     ]
   }
 }
\ No newline at end of file

tools/bowtie2/bowtie2.yaml

@@ -143,10 +143,10 @@
   },
   citations:  {
     bowtie2: [
-      "Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923"
+      "Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https://doi.org/10.1038/nmeth.1923"
     ],
     samtools: [
-      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
+      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
     ]
   }
 }
\ No newline at end of file

tools/bwa-mem2/bwa-mem2.yaml

@@ -120,7 +120,7 @@
       "Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019"
     ],
     samtools: [
-      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
+      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
     ]
   }
 }
\ No newline at end of file

tools/bwa/bwa.yaml

@@ -155,13 +155,13 @@
   },
   citations:  {
     bwa: [
-      "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754–1760, https://doi.org/10.1093/bioinformatics/btp324"
+      "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https://doi.org/10.1093/bioinformatics/btp324"
     ],
     bwa-mem: [
       "Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]"
     ],
     samtools: [
-      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
+      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https://doi.org/10.1093/bioinformatics/btp352"
     ]
   }
 }
\ No newline at end of file

tools/compare_vcfs_isec/compare_vcfs_isec.yaml

@@ -56,13 +56,13 @@
     },
   citations:  {
     bcftools: [
-      "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987–2993, https://doi.org/10.1093/bioinformatics/btr509"
+      "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https://doi.org/10.1093/bioinformatics/btr509"
     ],
     vcftools: [
       "The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http://dx.doi.org/10.1093/bioinformatics/btr330"
     ],
     upsetr: [
-      "Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014.doi: https://doi.org/10.1109/TVCG.2014.2346248"
+      "Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983-1992, 2014.doi: https://doi.org/10.1109/TVCG.2014.2346248"
     ]
   }
 }

tools/cstacks/cstacks.yaml

@@ -71,7 +71,7 @@
     },
   citations:  {
     stacks: [
-      " Rochette, NC, Rivera‐Colón, AG, Catchen, JM. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics.