diff --git a/.gitignore b/.gitignore
index f534691..1af936f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,8 @@ __pycache__/
 output/
 .parallel/
 .pytest_cache
+.cache
+.vscode
 
 # Files to ignore
 *.sif
diff --git a/Snakefile b/Snakefile
index e3ad38b..c7a3515 100644
--- a/Snakefile
+++ b/Snakefile
@@ -10,87 +10,105 @@ Date: 07-03-2022
 #################################################################################
 
 from yaml import safe_load
-import pathlib
+from pathlib import Path
 from shutil import copyfile
 
 #################################################################################
 #####                   Load samplesheet and config params                  #####
 #################################################################################
 
-# Loading sample sheet as dictionary 
+# Loading sample sheet as dictionary
 # ("R1" and "R2" keys for fastq)
 sample_sheet = config["sample_sheet"]
 SAMPLES = {}
 with open(sample_sheet) as sample_sheet_file:
-    SAMPLES = safe_load(sample_sheet_file) 
+    SAMPLES = safe_load(sample_sheet_file)
 
-GIVEN_REF=config['ref']
+GIVEN_REF = config["reference"]
 
-#@################################################################################
-#@####                         Expected output                               #####
-#@################################################################################
-output_dir = pathlib.Path(config["out"])
-log_dir = output_dir.joinpath('log')
-db_dir = pathlib.Path(config["db_dir"])
-mash_db = db_dir.joinpath('bacteria-refseq', 'db.msh')
-referenceseeker_md5 = str(db_dir.joinpath('bacteria-refseq', 'downloaded_db.txt'))
+#################################################################################
+#####                         Expected output                               #####
+#################################################################################
+output_dir = Path(config["output_dir"])
+log_dir = output_dir.joinpath("log")
+db_dir = Path(config["db_dir"])
+mash_db = db_dir.joinpath("bacteria-refseq", "db.msh")
+referenceseeker_md5 = str(db_dir.joinpath("bacteria-refseq", "downloaded_db.txt"))
 
-if config['dryrun'] is True and GIVEN_REF is not None:
+if (config["dryrun"] is True) and (GIVEN_REF != "None"):
     ref_genome = GIVEN_REF
 else:
-    ref_genome = output_dir.joinpath('ref_genomes_used', 'cluster_1', 'ref_genome.fasta')
+    ref_genome = output_dir.joinpath(
+        "ref_genomes_used", "cluster_1", "ref_genome.fasta"
+    )
 
-if GIVEN_REF is not None and not ref_genome.exists():
+# GIVEN_REF is converted to str
+if (GIVEN_REF != "None") and (not ref_genome.exists()):
+    print(f"Copying reference genome {GIVEN_REF} to {ref_genome}")
     output_dir.mkdir(exist_ok=True, parents=True)
     ref_dir = ref_genome.parent
     ref_dir.mkdir(exist_ok=True, parents=True)
     copyfile(GIVEN_REF, ref_genome)
 
+
 def get_output_per_cluster(cluster):
     with open(checkpoints.preclustering.get(**cluster).output[0]) as file:
         SAMPLE_CLUSTERS = yaml.safe_load(file)
-    CLUSTERS = set([ cluster for sample, cluster in SAMPLE_CLUSTERS.items() ])
-    output_files = expand(output_dir.joinpath('tree/cluster_{cluster}/{file}'),
-                    cluster=CLUSTERS,
-                    file=['newick_tree.txt', 'snp_matrix.csv'])
-    output_iqtree = expand(output_dir.joinpath('ml_tree', 'cluster_{cluster}'),
-                    cluster=CLUSTERS)
+    CLUSTERS = set([cluster for sample, cluster in SAMPLE_CLUSTERS.items()])
+    output_files = expand(
+        output_dir.joinpath("tree/cluster_{cluster}/{file}"),
+        cluster=CLUSTERS,
+        file=["newick_tree.txt", "snp_matrix.csv"],
+    )
+    output_iqtree = expand(
+        output_dir.joinpath("ml_tree", "cluster_{cluster}"), cluster=CLUSTERS
+    )
     return output_files + output_iqtree
 
 
-#@################################################################################
-#@####                              Processes                                #####
-#@################################################################################
+#################################################################################
+#####                              Processes                                #####
+#################################################################################
+
+if GIVEN_REF != "None":
 
-if GIVEN_REF is not None:
     include: "bin/rules/mock_cluster.smk"
+
 else:
+
     include: "bin/rules/pre_cluster.smk"
     include: "bin/rules/find_reference.smk"
 
+
 include: "bin/rules/snp_analysis.smk"
 include: "bin/rules/dm_n_viz.smk"
 
-#@################################################################################
-#@####              Finalize pipeline (error/success)                        #####
-#@################################################################################
+
+#################################################################################
+#####              Finalize pipeline (error/success)                        #####
+#################################################################################
+
 
 onerror:
-    shell("""
+    shell(
+        """
 rm -f tmp*npy
 rm -f tmp*_fastme_stat.txt
 rm -f tmp*_fastme_tree.nwk
 rm -f tmp*dist.list
 echo -e "Something went wrong with Juno-SNP pipeline. Please check the logging files in {output_dir}/log/"
-    """)
+    """
+    )
 
 
 #################################################################################
 #####                       Specify final output                            #####
 #################################################################################
 
+
 localrules:
-    all
+    all,
+
 
 rule all:
     input:
diff --git a/envs/juno_snp.yaml b/envs/juno_snp.yaml
new file mode 100644
index 0000000..bcb8d5e
--- /dev/null
+++ b/envs/juno_snp.yaml
@@ -0,0 +1,19 @@
+name: juno_snp
+channels:
+  - bioconda
+  - conda-forge
+  - nodefaults
+dependencies:
+  - git=2.40.*
+  - mamba==1.3.*
+  - pip>=21.2
+  - pandas==1.3.2
+  - python>3.7.6
+  - snakemake==7.32.0
+  - pytest
+  - biopython
+  - pip:
+    - numpy
+    - "--editable=git+https://github.com/RIVM-bioinformatics/juno-library.git@v2.1.3#egg=juno_library"
+
+
diff --git a/envs/master_env.yaml b/envs/master_env.yaml
deleted file mode 100644
index dcae50a..0000000
--- a/envs/master_env.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-name: juno_snp
-channels:
-  - bioconda
-  - conda-forge
-  - nodefaults
-dependencies:
-  - git
-  - mamba==0.24.0
-  - libmamba==0.24.0
-  - libmambapy==0.24.0
-  - libarchive==3.5.2
-  - pip>=21.2
-  - pandas==1.3.2
-  - python>3.7.6
-  - snakemake==7.18.2
-  - pytest
-  - pytest-cov
-  - biopython
-  - pip:
-    - numpy
-    - "--editable=git+https://github.com/RIVM-bioinformatics/base_juno_pipeline.git@v0.2.7#egg=base_juno"
-
-
diff --git a/juno_snp.py b/juno_snp.py
index 0517249..6c4abde 100644
--- a/juno_snp.py
+++ b/juno_snp.py
@@ -11,117 +11,185 @@
 """
 
 # Dependencies
-from base_juno_pipeline import base_juno_pipeline, helper_functions
+from juno_library import Pipeline
 import argparse
-import pathlib
-import subprocess
+from pathlib import Path
+from typing import Union, Callable
 import yaml
+from dataclasses import dataclass, field
+
 from version import __package_name__, __version__, __description__
 
-class JunoSnpRun(
-    base_juno_pipeline.PipelineStartup, base_juno_pipeline.RunSnakemake
-):
-    """Class with the arguments and specifications that are only for the Juno-typing pipeline but inherit from PipelineStartup and RunSnakemake"""
+def main() -> None:
+    juno_snp = JunoSnp()
+    juno_snp.run()
+
+def check_number_within_range(
+    minimum: float = 0, maximum: float = 1
+) -> Union[Callable[[str], str], argparse.FileType]:
+    """
+    Creates a function to check whether a numeric value is within a range, inclusive.
+
+    The generated function can be used by the `type` parameter in argparse.ArgumentParser.
+    See https://stackoverflow.com/a/53446178.
+
+    Args:
+        value: the numeric value to check.
+        minimum: minimum of allowed range, inclusive.
+        maximum: maximum of allowed range, inclusive.
+
+    Returns:
+        A function which takes a single argument and checks this against the range.
+
+    Raises:
+        argparse.ArgumentTypeError: if the value is outside the range.
+        ValueError: if the value cannot be converted to float.
+    """
+
+    def generated_func_check_range(value: str) -> str:
+        value_f = float(value)
+        if (value_f < minimum) or (value_f > maximum):
+            raise argparse.ArgumentTypeError(
+                f"Supplied value {value} is not within expected range {minimum} to {maximum}."
+            )
+        return str(value)
+
+    return generated_func_check_range
+
+
+@dataclass
+class JunoSnp(Pipeline):
     pipeline_name: str = __package_name__
     pipeline_version: str = __version__
+    input_type: str = 'both'
 
-    def __init__(self, 
-                input_dir, 
-                ref,
-                output_dir, 
-                db_dir='/mnt/db/juno/snp',
-                ani=0.95,
-                conserved_dna=0.69,
-                sliding_window=400,
-                kmer_length=21,
-                sketch_size=1000,
-                mash_threshold=0.01,
-                tree_algorithm='upgma',
-                cores=300,
-                time_limit=60,
-                local=False,
-                queue='bio',
-                unlock=False,
-                rerunincomplete=False,
-                dryrun=False,
-                run_in_container=True,
-                prefix=None,
-                **kwargs):
-        """Initiating Juno-SNP pipeline"""
-        
-        # Get proper file paths
-        output_dir = pathlib.Path(output_dir).resolve()
-        if ref is not None:
-            self.ref = pathlib.Path(ref).resolve()
-        else:
-            self.ref = None
-        self.db_dir = pathlib.Path(db_dir).resolve()
-        self.ani_threshold=float(ani)
-        self.conserved_dna_threshold=float(conserved_dna)
-        self.sliding_window=int(sliding_window)
-        self.kmer_length=int(kmer_length)
-        self.sketch_size=int(sketch_size)
-        self.mash_threshold=float(mash_threshold)
-        if tree_algorithm not in ['upgma', 'nj']:
-            raise ValueError(
-                f'The provided tree algorithm {tree_algorithm} is not supported.' \
-                ' Please choose upgma or nj'
-            )
-        self.tree_algorithm=tree_algorithm
-        workdir = pathlib.Path(__file__).parent.resolve()
-        self.path_to_audit = output_dir.joinpath('audit_trail')
-        base_juno_pipeline.PipelineStartup.__init__(
-            self,
-            input_dir=pathlib.Path(input_dir).resolve(), 
-            input_type='both',
-            min_num_lines=2
-        ) # Min for viable fasta
-        base_juno_pipeline.RunSnakemake.__init__(
-            self,
-            pipeline_name='Juno_SNP',
-            pipeline_version='v0.1',
-            output_dir=output_dir,
-            workdir=workdir,
-            cores=cores,
-            time_limit=time_limit,
-            local=local,
-            queue=queue,
-            unlock=unlock,
-            rerunincomplete=rerunincomplete,
-            dryrun=dryrun,
-            useconda=not run_in_container,
-            conda_prefix=prefix,
-            usesingularity=run_in_container,
-            singularityargs=f"--bind {self.input_dir}:{self.input_dir} --bind {output_dir}:{output_dir} --bind {self.db_dir}:{self.db_dir}",
-            singularity_prefix=prefix,
-            restarttimes=1,
-            latency_wait=60,
-            name_snakemake_report=str(self.path_to_audit.joinpath('juno_snp_report.html')),
-            **kwargs
+    def _add_args_to_parser(self) -> None:
+        super()._add_args_to_parser()
+
+        self.parser.description = __description__
+
+        self.add_argument(
+            "-r",
+            "--reference",
+            type = Path,
+            required = False,
+            metavar = "FILE",
+            help = "Relative or absolute path to a reference fasta file."
+        )
+        self.add_argument(
+            "-d",
+            "--db-dir",
+            type = Path,
+            metavar = "DIR",
+            default = "/mnt/db/juno/snp",
+            help = "Relative or absolute path to the database directory. If non is given, /mnt/db/juno/snp"\
+                " (where the default db resides at the RIVM will be used)."
+        )
+        self.add_argument(
+            "-a",
+            "--ani",
+            type = check_number_within_range(0, 1),
+            metavar = "INT",
+            default = 0.95,
+            help="ANI threshold. Passed to referenceseeker"
+        )
+        self.add_argument(
+            "-cd",
+            "--conserved-dna",
+            type = check_number_within_range(0, 1),
+            metavar = "INT",
+            default = 0.69,
+            help="Conserved DNA threshold. Passed to referenceseeker"
         )
+        self.add_argument(
+            "-sw",
+            "--sliding-window",
+            type = check_number_within_range(100, 1000),
+            metavar = "INT",
+            default = 400,
+            help="Sliding window - the lower the more accurate but also slower. Passed to referenceseeker"
+        )
+        self.add_argument(
+            "-kl",
+            "--kmer-length",
+            type = check_number_within_range(1, 32),
+            metavar = "INT",
+            default = 21,
+            help="K-mer length - longer kmers increase specificity, shorter kmers increase sensitivity. Passed to mash sketch"
+        )
+        self.add_argument(
+            "-ss",
+            "--sketch-size",
+            type = int,
+            metavar = "INT",
+            default = 1000,
+            help="Sketch size - larger sketch size better represents the original sequence," \
+                " but leads to large files and longer running time. Passed to mash sketch"
+        )
+        self.add_argument(
+            "-mt",
+            "--mash-threshold",
+            type = check_number_within_range(0, 1),
+            metavar = "FLOAT",
+            default = 0.01,
+            help="Mash threshold - maximum mash distance to consider genomes similar. Passed to preclustering script."
+        )
+        self.add_argument(
+            "-t",
+            "--tree-algorithm",
+            type = str,
+            metavar = "ALGORITHM",
+            default = 'upgma',
+            choices=['upgma', 'nj'],
+            help="Algorithm to use for making the tree. It can be 'upgma' or 'nj' (neighbor-joining). Default is upgma"
+        )
+
 
-        # Start pipeline
-        self.run_juno_snp_pipeline()
 
-    def start_juno_snp_pipeline(self):
-        """
-        Function to start the pipeline
-        """
-        self.start_juno_pipeline()
-        with open(self.sample_sheet, 'w') as file_:
-            yaml.dump(self.sample_dict, file_, default_flow_style=False)
+    def _parse_args(self) -> argparse.Namespace:
+        args = super()._parse_args()
+
+        self.reference: Path = args.reference
+        self.db_dir: Path = args.db_dir
+        self.ani: float = args.ani
+        self.conserved_dna: float = args.conserved_dna
+        self.sliding_window: int = args.sliding_window
+        self.kmer_length: int = args.kmer_length
+        self.sketch_size: int = args.sketch_size
+        self.mash_threshold: float = args.mash_threshold
+        self.tree_algorithm: str = args.tree_algorithm
+        self.dryrun: bool = args.dryrun
+
+        return args
     
-    def write_userparameters(self):
+    def setup(self) -> None:
+        super().setup()
+        if self.snakemake_args["use_singularity"]:
+            self.snakemake_args["singularity_args"] = " ".join(
+                [
+                    self.snakemake_args["singularity_args"],
+                    f"--bind {self.db_dir}:{self.db_dir}",
+                ]  # paths that singularity should be able to read from can be bound by adding to the above list
+            )
 
-        config_params = {
-            'input_dir': str(self.input_dir),
-            'ref': self.ref,
-            'out': str(self.output_dir),
-            'db_dir': str(self.db_dir),
+        with open(
+            Path(__file__).parent.joinpath("config/pipeline_parameters.yaml")
+        ) as f:
+            parameters_dict = yaml.safe_load(f)
+        self.snakemake_config.update(parameters_dict)
+
+        self.user_parameters = {
+            "input_dir": str(self.input_dir),
+            "output_dir": str(self.output_dir),
+            "exclusion_file": str(self.exclusion_file),
+            "db_dir": str(self.db_dir),
+            "reference": str(self.reference),
+            "use_singularity": str(self.snakemake_args["use_singularity"]),
+            'dryrun': self.dryrun,
             'referenceseeker': {
                 'db': str(self.db_dir.joinpath('bacteria-refseq')),
-                'ani_threshold': self.ani_threshold,
-                'conserved_dna_threshold': self.conserved_dna_threshold,
+                'ani_threshold': self.ani,
+                'conserved_dna_threshold': self.conserved_dna,
                 'sliding_window': self.sliding_window
             },
             'mash': {
@@ -132,249 +200,212 @@ def write_userparameters(self):
             'tree': {
                 'algorithm' : self.tree_algorithm
             },
-            'dryrun': self.dryrun
         }
+
+
+if __name__ == "__main__":
+    main()
+
+
+
+# class JunoSnpRun(
+#     base_juno_pipeline.PipelineStartup, base_juno_pipeline.RunSnakemake
+# ):
+#     """Class with the arguments and specifications that are only for the Juno-typing pipeline but inherit from PipelineStartup and RunSnakemake"""
+#     pipeline_name: str = __package_name__
+#     pipeline_version: str = __version__
+
+#     def __init__(self, 
+#                 input_dir, 
+#                 ref,
+#                 output_dir, 
+#                 db_dir='/mnt/db/juno/snp',
+#                 ani=0.95,
+#                 conserved_dna=0.69,
+#                 sliding_window=400,
+#                 kmer_length=21,
+#                 sketch_size=1000,
+#                 mash_threshold=0.01,
+#                 tree_algorithm='upgma',
+#                 cores=300,
+#                 time_limit=60,
+#                 local=False,
+#                 queue='bio',
+#                 unlock=False,
+#                 rerunincomplete=False,
+#                 dryrun=False,
+#                 run_in_container=True,
+#                 prefix=None,
+#                 **kwargs):
+#         """Initiating Juno-SNP pipeline"""
         
-        with open(self.user_parameters, 'w') as file_:
-            yaml.dump(config_params, file_, default_flow_style=False)
+#         # Get proper file paths
+#         output_dir = pathlib.Path(output_dir).resolve()
+#         if ref is not None:
+#             self.ref = pathlib.Path(ref).resolve()
+#         else:
+#             self.ref = None
+#         self.db_dir = pathlib.Path(db_dir).resolve()
+#         self.ani_threshold=float(ani)
+#         self.conserved_dna_threshold=float(conserved_dna)
+#         self.sliding_window=int(sliding_window)
+#         self.kmer_length=int(kmer_length)
+#         self.sketch_size=int(sketch_size)
+#         self.mash_threshold=float(mash_threshold)
+#         if tree_algorithm not in ['upgma', 'nj']:
+#             raise ValueError(
+#                 f'The provided tree algorithm {tree_algorithm} is not supported.' \
+#                 ' Please choose upgma or nj'
+#             )
+#         self.tree_algorithm=tree_algorithm
+#         workdir = pathlib.Path(__file__).parent.resolve()
+#         self.path_to_audit = output_dir.joinpath('audit_trail')
+#         base_juno_pipeline.PipelineStartup.__init__(
+#             self,
+#             input_dir=pathlib.Path(input_dir).resolve(), 
+#             input_type='both',
+#             min_num_lines=2
+#         ) # Min for viable fasta
+#         base_juno_pipeline.RunSnakemake.__init__(
+#             self,
+#             pipeline_name='Juno_SNP',
+#             pipeline_version='v0.1',
+#             output_dir=output_dir,
+#             workdir=workdir,
+#             cores=cores,
+#             time_limit=time_limit,
+#             local=local,
+#             queue=queue,
+#             unlock=unlock,
+#             rerunincomplete=rerunincomplete,
+#             dryrun=dryrun,
+#             useconda=not run_in_container,
+#             conda_prefix=prefix,
+#             usesingularity=run_in_container,
+#             singularityargs=f"--bind {self.input_dir}:{self.input_dir} --bind {output_dir}:{output_dir} --bind {self.db_dir}:{self.db_dir}",
+#             singularity_prefix=prefix,
+#             restarttimes=1,
+#             latency_wait=60,
+#             name_snakemake_report=str(self.path_to_audit.joinpath('juno_snp_report.html')),
+#             **kwargs
+#         )
+
+#         # Start pipeline
+#         self.run_juno_snp_pipeline()
 
-        return config_params     
+#     def start_juno_snp_pipeline(self):
+#         """
+#         Function to start the pipeline
+#         """
+#         self.start_juno_pipeline()
+#         with open(self.sample_sheet, 'w') as file_:
+#             yaml.dump(self.sample_dict, file_, default_flow_style=False)
+    
+#     def write_userparameters(self):
+
+#         config_params = {
+#             'input_dir': str(self.input_dir),
+#             'ref': self.ref,
+#             'out': str(self.output_dir),
+#             'db_dir': str(self.db_dir),
+#             'referenceseeker': {
+#                 'db': str(self.db_dir.joinpath('bacteria-refseq')),
+#                 'ani_threshold': self.ani_threshold,
+#                 'conserved_dna_threshold': self.conserved_dna_threshold,
+#                 'sliding_window': self.sliding_window
+#             },
+#             'mash': {
+#                 'kmer_length': self.kmer_length,
+#                 'sketch_size': self.sketch_size,
+#                 'threshold': self.mash_threshold
+#             },
+#             'tree': {
+#                 'algorithm' : self.tree_algorithm
+#             },
+#             'dryrun': self.dryrun
+#         }
         
-    def run_juno_snp_pipeline(self):
-        self.start_juno_snp_pipeline()
-        self.user_params = self.write_userparameters()
-        self.get_run_info()
-        if not self.dryrun or self.unlock:
-            self.path_to_audit.mkdir(parents=True, exist_ok=True)
-
-        self.successful_run = self.run_snakemake()
-        assert self.successful_run, f'Please check the log files'
-        if not self.dryrun or self.unlock:
-            subprocess.run(
-                ['find', self.output_dir, '-type', 'f', '-empty', '-exec', 'rm', '{}', ';']
-            )
-            subprocess.run(
-                ['find', self.output_dir, '-type', 'd', '-empty', '-exec', 'rm', '-rf', '{}', ';']
-            )
-            self.make_snakemake_report()
-
-def check_sliding_window(num):
-    num_int = int(num)
-    if num_int > 99 and num_int < 1001:
-        return num_int
-    else:
-        raise ValueError(
-            f'The provided input value for sliding window {str(num)} is not valid.' \
-            ' Please provide a number between 100-1000'
-        )
+#         with open(self.user_parameters, 'w') as file_:
+#             yaml.dump(config_params, file_, default_flow_style=False)
 
-def check_between_zero_and_one(num):
-    num_f = float(num)
-    if num_f >= 0 and num_f <= 1:
-        return num_f
-    else:
-        raise ValueError(
-            f'The provided input value {str(num)} is not valid. '\
-            'Please provide a value between 0-1'
-        )
+#         return config_params     
+        
+#     def run_juno_snp_pipeline(self):
+#         self.start_juno_snp_pipeline()
+#         self.user_params = self.write_userparameters()
+#         self.get_run_info()
+#         if not self.dryrun or self.unlock:
+#             self.path_to_audit.mkdir(parents=True, exist_ok=True)
 
-def check_kmer_length(num):
-    num_int = int(num)
-    if num_int >= 1 and num_int <= 32:
-        return num_int
-    else:
-        raise ValueError(
-            f'The provided input value for kmer length {str(num)} is not valid.' \
-            ' Please provide a number between 1-32'
-        )
+#         self.successful_run = self.run_snakemake()
+#         assert self.successful_run, f'Please check the log files'
+#         if not self.dryrun or self.unlock:
+#             subprocess.run(
+#                 ['find', self.output_dir, '-type', 'f', '-empty', '-exec', 'rm', '{}', ';']
+#             )
+#             subprocess.run(
+#                 ['find', self.output_dir, '-type', 'd', '-empty', '-exec', 'rm', '-rf', '{}', ';']
+#             )
+#             self.make_snakemake_report()
+
+# def check_sliding_window(num):
+#     num_int = int(num)
+#     if num_int > 99 and num_int < 1001:
+#         return num_int
+#     else:
+#         raise ValueError(
+#             f'The provided input value for sliding window {str(num)} is not valid.' \
+#             ' Please provide a number between 100-1000'
+#         )
+
+# def check_between_zero_and_one(num):
+#     num_f = float(num)
+#     if num_f >= 0 and num_f <= 1:
+#         return num_f
+#     else:
+#         raise ValueError(
+#             f'The provided input value {str(num)} is not valid. '\
+#             'Please provide a value between 0-1'
+#         )
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(
-        description = __description__,
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
-    )
-    parser.add_argument(
-        "-i",
-        "--input",
-        type = pathlib.Path,
-        required = True,
-        metavar = "DIR",
-        help = "Relative or absolute path to the input directory. It must either be the output directory of the Juno-assembly pipeline or it must contain all the raw reads (fastq) and assemblies (fasta) files for all samples to be processed."
-    )
-    parser.add_argument(
-        "-r",
-        "--reference",
-        type = pathlib.Path,
-        required = False,
-        metavar = "FILE",
-        help = "Relative or absolute path to a reference fasta file."
-    )
-    parser.add_argument(
-        "-o",
-        "--output",
-        type = pathlib.Path,
-        metavar = "DIR",
-        default = "output",
-        help = "Relative or absolute path to the output directory. If non is given, an 'output' directory will be created in the current directory."
-    )
-    parser.add_argument(
-        "-d",
-        "--db-dir",
-        type = pathlib.Path,
-        metavar = "DIR",
-        default = "/mnt/db/juno/snp",
-        help = "Relative or absolute path to the database directory. If non is given, /mnt/db/juno/snp"\
-            " (where the default db resides at the RIVM will be used)."
-    )
-    parser.add_argument(
-        "-a",
-        "--ani",
-        type = check_between_zero_and_one,
-        metavar = "INT",
-        default = 0.95,
-        help="ANI threshold. Passed to referenceseeker"
-    )
-    parser.add_argument(
-        "-cd",
-        "--conserved-dna",
-        type = check_between_zero_and_one,
-        metavar = "INT",
-        default = 0.69,
-        help="Conserved DNA threshold. Passed to referenceseeker"
-    )
-    parser.add_argument(
-        "-sw",
-        "--sliding-window",
-        type = check_sliding_window,
-        metavar = "INT",
-        default = 400,
-        help="Sliding window - the lower the more accurate but also slower. Passed to referenceseeker"
-    )
-    parser.add_argument(
-        "-kl",
-        "--kmer-length",
-        type = check_kmer_length,
-        metavar = "INT",
-        default = 21,
-        help="K-mer length - longer kmers increase specificity, shorter kmers increase sensitivity. Passed to mash sketch"
-    )
-    parser.add_argument(
-        "-ss",
-        "--sketch-size",
-        type = int,
-        metavar = "INT",
-        default = 1000,
-        help="Sketch size - larger sketch size better represents the original sequence," \
-            " but leads to large files and longer running time. Passed to mash sketch"
-    )
-    parser.add_argument(
-        "-mt",
-        "--mash-threshold",
-        type = check_between_zero_and_one,
-        metavar = "FLOAT",
-        default = 0.01,
-        help="Mash threshold - maximum mash distance to consider genomes similar. Passed to preclustering script."
-    )
-    parser.add_argument(
-        "-t",
-        "--tree-algorithm",
-        type = str,
-        metavar = "ALGORITHM",
-        default = 'upgma',
-        choices=['upgma', 'nj'],
-        help="Algorithm to use for making the tree. It can be 'upgma' or 'nj' (neighbor-joining). Default is upgma"
-    )
-    parser.add_argument(
-        "--no-containers",
-        action = 'store_false',
-        help = "Use conda environments instead of containers."
-    )
-    parser.add_argument(
-        "-p",
-        "--prefix",
-        type = str,
-        metavar="PATH",
-        default=None,
-        help = "Conda or singularity prefix. Path to the place where you want to store the conda environments or the singularity images."
-    )
-    parser.add_argument(
-        "-c",
-        "--cores",
-        type = int,
-        metavar = "INT",
-        default = 300,
-        help="Number of cores to use. Default is 300"
-    )
-    #TODO: Get from ${irods_runsheet_sys__runsheet__lsf_queue} if it exists
-    parser.add_argument(
-        "-q",
-        "--queue",
-        type = str,
-        metavar = "STR",
-        default = 'bio',
-        help = 'Name of the queue that the job will be submitted to if working on a cluster.'
-    )
-    parser.add_argument(
-        "-l",
-        "--local",
-        action='store_true',
-        help="Running pipeline locally (instead of in a computer cluster). Default is running it in a cluster."
-    )
-    parser.add_argument(
-        "-w",
-        "--time-limit",
-        type = int,
-        metavar = "INT",
-        default = 60,
-        help="Time limit per job in minutes (passed as -W argument to bsub). Jobs will be killed if not finished in this time."
-    )
-    # Snakemake arguments
-    parser.add_argument(
-        "-u",
-        "--unlock",
-        action = 'store_true',
-        help = "Unlock output directory (passed to snakemake)."
-    )
-    parser.add_argument(
-        "-n",
-        "--dryrun",
-        action='store_true',
-        help="Dry run printing steps to be taken in the pipeline without actually running it (passed to snakemake)."
-    )
-    parser.add_argument(
-        "--rerunincomplete",
-        action='store_true',
-        help="Re-run jobs if they are marked as incomplete (passed to snakemake)."
-    )
-    parser.add_argument(
-        "--snakemake-args",
-        nargs='*',
-        default={},
-        action=helper_functions.SnakemakeKwargsAction,
-        help="Extra arguments to be passed to snakemake API (https://snakemake.readthedocs.io/en/stable/api_reference/snakemake.html)."
-    )
-    parser.add_argument('--version', action='version', version=f'{__package_name__} {__version__}')
-    args = parser.parse_args()
-    JunoSnpRun(
-        input_dir=args.input, 
-        ref=args.reference,
-        output_dir=args.output,
-        db_dir=args.db_dir,
-        ani=args.ani,
-        conserved_dna=args.conserved_dna,
-        sliding_window=args.sliding_window,
-        kmer_length=args.kmer_length,
-        sketch_size=args.sketch_size,
-        mash_threshold=args.mash_threshold,
-        tree_algorithm=args.tree_algorithm,
-        cores=args.cores,
-        local=args.local,
-        time_limit=args.time_limit,
-        queue=args.queue,
-        unlock=args.unlock,
-        rerunincomplete=args.rerunincomplete,
-        dryrun=args.dryrun,
-        run_in_container=args.no_containers,
-        prefix=args.prefix,
-        **args.snakemake_args
-    )
+# def check_kmer_length(num):
+#     num_int = int(num)
+#     if num_int >= 1 and num_int <= 32:
+#         return num_int
+#     else:
+#         raise ValueError(
+#             f'The provided input value for kmer length {str(num)} is not valid.' \
+#             ' Please provide a number between 1-32'
+#         )
+
+# if __name__ == '__main__':
+#     parser = argparse.ArgumentParser(
+#         description = __description__,
+#         formatter_class=argparse.ArgumentDefaultsHelpFormatter
+#     )
+    
+#     parser.add_argument('--version', action='version', version=f'{__package_name__} {__version__}')
+#     args = parser.parse_args()
+#     JunoSnpRun(
+#         input_dir=args.input, 
+#         ref=args.reference,
+#         output_dir=args.output,
+#         db_dir=args.db_dir,
+#         ani=args.ani,
+#         conserved_dna=args.conserved_dna,
+#         sliding_window=args.sliding_window,
+#         kmer_length=args.kmer_length,
+#         sketch_size=args.sketch_size,
+#         mash_threshold=args.mash_threshold,
+#         tree_algorithm=args.tree_algorithm,
+#         cores=args.cores,
+#         local=args.local,
+#         time_limit=args.time_limit,
+#         queue=args.queue,
+#         unlock=args.unlock,
+#         rerunincomplete=args.rerunincomplete,
+#         dryrun=args.dryrun,
+#         run_in_container=args.no_containers,
+#         prefix=args.prefix,
+#         **args.snakemake_args
+#     )