diff --git a/.deprecated/align-minimap.smk b/.deprecated/align-minimap.smk
index 055a3dc63..a91fcc789 100644
--- a/.deprecated/align-minimap.smk
+++ b/.deprecated/align-minimap.smk
@@ -234,12 +234,12 @@ rule assign_molecules:
         bai = outdir + "/{sample}.bam.bai"
     params:
         molecule_distance
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Assigning barcodes to molecules: {wildcards.sample}"
-    script:
-        "scripts/assignMI.py"
+    shell:
+        "assignMI.py -o {output.bam} -c {params} {input.bam}"
 
 rule alignment_bxstats:
     input:
@@ -249,12 +249,12 @@ rule alignment_bxstats:
         outdir + "/reports/data/bxstats/{sample}.bxstats.gz"
     params:
         sample = lambda wc: d[wc.sample]
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Calculating barcode alignment statistics: {wildcards.sample}"
-    script:
-        "scripts/bxStats.py"
+    shell:
+        "bxStats.py -o {output} {input.bam}"
 
 rule alignment_coverage:
     input: 
diff --git a/.github/filters.yml b/.github/filters.yml
index a232a00b6..3cc4233f4 100644
--- a/.github/filters.yml
+++ b/.github/filters.yml
@@ -18,8 +18,8 @@ preflight: &preflight
   - 'src/harpy/rules/preflight-bam.smk'
   - 'test/fastq/**'
   - 'test/bam/**'
-  - 'src/harpy/scripts/checkBAM.py'
-  - 'src/harpy/scripts/checkFASTQ.py'
+  - 'src/harpy/bin/checkBAM.py'
+  - 'src/harpy/bin/checkFASTQ.py'
   - 'src/harpy/reports/PreflightFastq.Rmd'
   - 'src/harpy/reports/PreflightBam.Rmd'
 demux: &demux
@@ -43,8 +43,9 @@ bwa: &bwa
   - 'src/harpy/rules/align-bwa.smk'
   - 'src/harpy/reports/AlignStats.Rmd'
   - 'src/harpy/reports/BxCount.Rmd'
-  - 'src/harpy/scripts/bxStats.py'
-  - 'src/harpy/scripts/countBX.py'
+  - 'src/harpy/bin/bxStats.py'
+  - 'src/harpy/bin/countBX.py'
+  - 'src/harpy/bin/assignMI.py'
   - 'src/harpy/bin/makeWindows.py'
   - 'test/fastq/**'
 ema: &ema
@@ -53,10 +54,9 @@ ema: &ema
   - 'src/harpy/align.py'
   - 'src/harpy/rules/align-ema.smk'
   - 'src/harpy/reports/AlignStats.Rmd'
-  - 'src/harpy/reports/EmaCount.Rmd'
   - 'src/harpy/reports/BxCount.Rmd'
-  - 'src/harpy/scripts/bxStats.py'
-  - 'src/harpy/scripts/countBX.py'
+  - 'src/harpy/bin/bxStats.py'
+  - 'src/harpy/bin/countBX.py'
   - 'src/harpy/bin/makewindows.py'
   - 'test/fastq/**'
 strobealign: &strobealign
@@ -66,8 +66,9 @@ strobealign: &strobealign
   - 'src/harpy/rules/align-strobealign.smk'
   - 'src/harpy/reports/AlignStats.Rmd'
   - 'src/harpy/reports/BxCount.Rmd'
-  - 'src/harpy/scripts/bxStats.py'
-  - 'src/harpy/scripts/countBX.py'
+  - 'src/harpy/bin/assignMI.py'
+  - 'src/harpy/bin/bxStats.py'
+  - 'src/harpy/bin/countBX.py'
   - 'src/harpy/bin/makewindows.py'
   - 'test/fastq/**'
 mpileup: &mpileup
diff --git a/resources/harpy.yaml b/resources/harpy.yaml
index d3fc6ae47..129fe6d02 100644
--- a/resources/harpy.yaml
+++ b/resources/harpy.yaml
@@ -7,6 +7,7 @@ dependencies:
   - bcftools =1.20
   - mamba
   - pandas
+  - pysam
   - python
   - rich-click
   - snakemake-minimal >7
diff --git a/resources/meta.yaml b/resources/meta.yaml
index e002472f1..88ccdfb59 100644
--- a/resources/meta.yaml
+++ b/resources/meta.yaml
@@ -34,6 +34,7 @@ requirements:
     - apptainer
     - bcftools =1.20
     - pandas
+    - pysam
     - python >3.10
     - rich-click
     - snakemake-minimal >7
diff --git a/src/harpy/align.py b/src/harpy/align.py
index a0e03f29c..4342161d6 100644
--- a/src/harpy/align.py
+++ b/src/harpy/align.py
@@ -116,8 +116,6 @@ def bwa(inputs, output_dir, genome, depth_window, threads, extra_params, quality
     fqlist, sample_count = parse_fastq_inputs(inputs)
     validate_input_by_ext(genome, "--genome", [".fasta", ".fa", ".fasta.gz", ".fa.gz"])
     fetch_rule(workflowdir, "align-bwa.smk")
-    fetch_script(workflowdir, "assignMI.py")
-    fetch_script(workflowdir, "bxStats.py")
     fetch_report(workflowdir, "AlignStats.Rmd")
     fetch_report(workflowdir, "AlignBxStats.Rmd")
 
@@ -208,7 +206,6 @@ def ema(inputs, output_dir, platform, whitelist, genome, depth_window, threads,
     fqlist, sample_count = parse_fastq_inputs(inputs)
     validate_input_by_ext(genome, "--genome", [".fasta", ".fa", ".fasta.gz", ".fa.gz"])
     fetch_rule(workflowdir, "align-ema.smk")
-    fetch_script(workflowdir, "bxStats.py")
     fetch_report(workflowdir, "AlignStats.Rmd")
     fetch_report(workflowdir, "AlignBxStats.Rmd")
 
@@ -289,8 +286,6 @@ def strobe(inputs, output_dir, genome, read_length, depth_window, threads, extra
     fqlist, sample_count = parse_fastq_inputs(inputs)
     validate_input_by_ext(genome, "--genome", [".fasta", ".fa", ".fasta.gz", ".fa.gz"])
     fetch_rule(workflowdir, "align-strobealign.smk")
-    fetch_script(workflowdir, "assignMI.py")
-    fetch_script(workflowdir, "bxStats.py")
     fetch_report(workflowdir, "AlignStats.Rmd")
     fetch_report(workflowdir, "AlignBxStats.Rmd")
 
diff --git a/src/harpy/scripts/assignMI.py b/src/harpy/bin/assignMI.py
similarity index 80%
rename from src/harpy/scripts/assignMI.py
rename to src/harpy/bin/assignMI.py
index 10f85ee35..f8ab52809 100755
--- a/src/harpy/scripts/assignMI.py
+++ b/src/harpy/bin/assignMI.py
@@ -1,29 +1,34 @@
+#! /usr/bin/env python
+
 import re
 import os
 import sys
+import argparse
 import pysam
-#import argparse
-
-#parser = argparse.ArgumentParser(
-#    prog = 'assignMI.py',
-#    description = 
-#    """
-#    Assign an MI:i: (Molecular Identifier) tag to each barcoded 
-#    record based on a molecular distance cutoff. Unmapped records
-#    are discarded in the output. Records without a BX:Z: tag or
-#    with an invalid barcode (00 as one of its segments) are presevered
-#    but are not assigned an MI:i tag. Input file MUST BE COORDINATE SORTED.
-#    """,
-#    usage = "assignMI.py -c cutoff -i input.bam -o output.bam",
-#    exit_on_error = False
-#    )
-#parser.add_argument('-c','--cutoff', type=int, default = 100000, help = "Distance in base pairs at which alignments with the same barcode should be considered different molecules. (default: 100000)")
-#parser.add_argument('-i', '--input', help = "Input coordinate-sorted bam/sam file. If bam, a matching index file should be in the same directory.")
-#parser.add_argument('-o', '--output', help = "Output bam file. Will also create an index file.")
-#
-#if len(sys.argv) == 1:
-#    parser.print_help(sys.stderr)
-#    sys.exit(1)
+
+parser = argparse.ArgumentParser(
+    prog = 'assignMI.py',
+    description =
+    """
+    Assign an MI:i: (Molecular Identifier) tag to each barcoded
+    record based on a molecular distance cutoff. Unmapped records
+    are discarded in the output. Records without a BX:Z: tag or
+    with an invalid barcode (00 as one of its segments) are presevered
+    but are not assigned an MI:i tag. Input file MUST BE COORDINATE SORTED.
+    """,
+    usage = "assignMI.py -c cutoff -o output.bam input.bam",
+    exit_on_error = False
+    )
+
+parser.add_argument('-c','--cutoff', type=int, default = 100000, help = "Distance in base pairs at which alignments with the same barcode should be considered different molecules. (default: 100000)")
+parser.add_argument('-o', '--output', help = "Output bam file. Will also create an index file.")
+parser.add_argument('input', help = "Input coordinate-sorted bam/sam file. If bam, a matching index file should be in the same directory.")
+
+if len(sys.argv) == 1:
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+
+args = parser.parse_args()
 
 def write_validbx(bam, alnrecord, molID):
     '''
@@ -97,7 +102,7 @@ def write_missingbx(bam, alnrecord):
     bam.write(alnrecord)
 
 #args = parser.parse_args()
-bam_input = snakemake.input[0]
+bam_input = args.input
 # initialize the dict
 d = dict()
 # chromlast keeps track of the last chromosome so we can
@@ -117,17 +122,15 @@ def write_missingbx(bam, alnrecord):
 alnfile = pysam.AlignmentFile(bam_input)
 
 # iniitalize output file
-#alnfile = pysam.AlignmentFile("/home/pdimens/Documents/harpy/test/bam/sample1.bam")
-outfile = pysam.AlignmentFile(snakemake.output[0], "wb", template = alnfile)
-#outfile = pysam.AlignmentFile("/home/pdimens/Documents/harpy/test/bam/test.bam", "w", template = alnfile)
+outfile = pysam.AlignmentFile(args.output, "wb", template = alnfile)
 
 for record in alnfile.fetch():
     chrm = record.reference_name
     bp   = record.query_alignment_length
     # check if the current chromosome is different from the previous one
     # if so, empty the dict (a consideration for RAM usage)
-    if chromlast != False and chrm != chromlast:
-        d = dict()
+    if chromlast is not False and chrm != chromlast:
+        d = {}
     if record.is_unmapped:
         # skip, don't output
         chromlast = chrm
@@ -146,7 +149,7 @@ def write_missingbx(bam, alnrecord):
         write_missingbx(outfile, record)
         chromlast = chrm
         continue
-    
+
     aln = record.get_blocks()
     if not aln:
         # unaligned, skip and don't output
@@ -160,9 +163,9 @@ def write_missingbx(bam, alnrecord):
     pos_end   = aln[-1][1]
 
     # create bx entry if it's not present
-    if bx not in d.keys():
+    if bx not in d:
         # increment MI b/c it's a new molecule
-        MI += 1 
+        MI += 1
         d[bx] = {
             "lastpos" : pos_end,
             "current_suffix": 0,
@@ -184,9 +187,9 @@ def write_missingbx(bam, alnrecord):
     # if the distance between alignments is > cutoff, it's a different molecule
     # so we'll +1 the suffix of the original barcode and relabel this one as 
     # BX + suffix. Since it's a new entry, we initialize it and move on
-    if dist > snakemake.params[0]:
+    if dist > args.cutoff:
         # increment MI b/c it's a new molecule
-        MI += 1 
+        MI += 1
         # increment original barcode's suffix
         d[orig]["current_suffix"] += 1
         bx = orig + "." + str(d[orig]["current_suffix"])
@@ -216,4 +219,4 @@ def write_missingbx(bam, alnrecord):
 outfile.close()
 
 # index the output file
-pysam.index(snakemake.output[0])
\ No newline at end of file
+pysam.index(args.output)
\ No newline at end of file
diff --git a/src/harpy/scripts/bxStats.py b/src/harpy/bin/bxStats.py
similarity index 78%
rename from src/harpy/scripts/bxStats.py
rename to src/harpy/bin/bxStats.py
index fae907bf8..5cf2c4c45 100755
--- a/src/harpy/scripts/bxStats.py
+++ b/src/harpy/bin/bxStats.py
@@ -1,9 +1,38 @@
+#! /usr/bin/env python
+
 import re
+import sys
 import gzip
+import argparse
 import pysam
 
-alnfile = pysam.AlignmentFile(snakemake.input[0])
-outfile = gzip.open(snakemake.output[0], "wb", 6)
+parser = argparse.ArgumentParser(
+    prog = 'bxStats.py',
+    description =
+    """
+    Calculates various linked-read molecule metrics from the input alignment file.
+    Metrics include (per molecule): number of reads, position start, position end,
+    length of molecule inferred from alignments, total aligned basepairs, total,
+    length of inferred inserts, molecule coverage (%) based on aligned bases, molecule
+    coverage (%) based on total inferred insert length.
+    Input file MUST BE COORDINATE SORTED.
+    """,
+    usage = "bxStats.py -o output.gz input.bam",
+    exit_on_error = False
+    )
+
+parser.add_argument('-o', '--output', help = "Gzipped tab-delimited file of metrics.")
+parser.add_argument('input', help = "Input coordinate-sorted bam/sam file. If bam, a matching index file should be in the same directory.")
+
+if len(sys.argv) == 1:
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+
+args = parser.parse_args()
+
+
+alnfile = pysam.AlignmentFile(args.input)
+outfile = gzip.open(args.output, "wb", 6)
 outfile.write(b"contig\tmolecule\treads\tstart\tend\tlength_inferred\taligned_bp\tinsert_len\tcoverage_bp\tcoverage_inserts\n")
 
 d = {}
diff --git a/src/harpy/scripts/checkBAM.py b/src/harpy/bin/checkBAM.py
similarity index 58%
rename from src/harpy/scripts/checkBAM.py
rename to src/harpy/bin/checkBAM.py
index e009e6746..d6844f423 100755
--- a/src/harpy/scripts/checkBAM.py
+++ b/src/harpy/bin/checkBAM.py
@@ -1,9 +1,33 @@
-import pysam
-import sys
+#! /usr/bin/env python
+
 import re
-import os.path
+import sys
+import os
+import argparse
+import pysam
+
+parser = argparse.ArgumentParser(
+    prog = 'checkBAM.py',
+    description =
+    """
+    Parses an aligment (sam/bam) file to check if the sample name
+    matched the RG tag, whether BX:Z: is the last tag in the record,
+    and the counts of: total alignments, alignments with an MI:i: tag,
+    alignments without BX:Z: tag, incorrect BX:Z: tag.
+    """,
+    usage = "checkBAM.py input.bam > output.txt",
+    exit_on_error = False
+    )
+
+parser.add_argument('input', help = "Input bam/sam file. If bam, a matching index file should be in the same directory.")
+
+if len(sys.argv) == 1:
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+
+args = parser.parse_args()
 
-bam_in = snakemake.input[0]
+bam_in = args.input
 
 # regex for EXACTLY AXXCXXBXXDXX
 haplotag = re.compile('^A[0-9][0-9]C[0-9][0-9]B[0-9][0-9]D[0-9][0-9]$')
@@ -46,5 +70,4 @@
 
 
 values = [str(i) for i in [os.path.basename(bam_in), nameMismatch, n_reads, noMI, noBX, badBX, bxNotLast]]
-with open(snakemake.output[0], "w") as fout:
-    print("\t".join(values), file = fout) 
\ No newline at end of file
+print("\t".join(values), file = sys.stdout)
diff --git a/src/harpy/scripts/checkFASTQ.py b/src/harpy/bin/checkFASTQ.py
similarity index 63%
rename from src/harpy/scripts/checkFASTQ.py
rename to src/harpy/bin/checkFASTQ.py
index 01666fa09..ff36f1ae3 100755
--- a/src/harpy/scripts/checkFASTQ.py
+++ b/src/harpy/bin/checkFASTQ.py
@@ -1,9 +1,32 @@
-import pysam
-import sys
+#! /usr/bin/env python
+
 import re
-import os.path
+import os
+import sys
+import argparse
+import pysam
+
+parser = argparse.ArgumentParser(
+    prog = 'checkFASTQ.py',
+    description =
+    """
+    Parses a FASTQ file to check if any sequences don't conform to the SAM spec,
+    whether BX:Z: is the last tag in the record, and the counts of: total reads,
+    reads without BX:Z: tag, reads with incorrect BX:Z: tag.
+    """,
+    usage = "checkBAM.py input.bam > output.txt",
+    exit_on_error = False
+    )
+
+parser.add_argument('input', help = "Input fastq file. Can be gzipped.")
+
+if len(sys.argv) == 1:
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+
+args = parser.parse_args()
 
-fq_in = snakemake.input[0]
+fq_in = args.input
 
 #bxz = re.compile('BX:Z:')
 samspec = re.compile('[A-Z][A-Z]:[AifZHB]:')
@@ -38,5 +61,4 @@
             noBX += 1
 
 values = [str(i) for i in [os.path.basename(fq_in), n_reads, noBX, badBX, badSamSpec, bxNotLast]]
-with open(snakemake.output[0], "w") as fout:
-    print("\t".join(values), file = fout) 
\ No newline at end of file
+print("\t".join(values), file = sys.stdout)
diff --git a/src/harpy/scripts/countBX.py b/src/harpy/bin/countBX.py
similarity index 51%
rename from src/harpy/scripts/countBX.py
rename to src/harpy/bin/countBX.py
index 09132fae6..6b47aa279 100755
--- a/src/harpy/scripts/countBX.py
+++ b/src/harpy/bin/countBX.py
@@ -1,6 +1,29 @@
-import pysam
+#! /usr/bin/env python
+
 import re
 import sys
+import argparse
+import pysam
+
+parser = argparse.ArgumentParser(
+    prog = 'countBX.py',
+    description =
+    """
+    Parses a FASTQ file to count: total sequences, total number of BX tags,
+    number of valid haplotagging BX tags, number of invalid BX tags, number of
+    invalid BX tag segments (i.e. A00, C00, B00, D00)
+    """,
+    usage = "countBX.py input.fastq > output.txt",
+    exit_on_error = False
+    )
+
+parser.add_argument('input', help = "Input fastq file. Can be gzipped.")
+
+if len(sys.argv) == 1:
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+
+args = parser.parse_args()
 
 n_reads = 0
 n_bx = 0
@@ -16,7 +39,7 @@
     "C" : 0,
     "D" : 0
 }
-with pysam.FastxFile(snakemake.input[0]) as fh:
+with pysam.FastxFile(args.input) as fh:
     for entry in fh:
         n_reads += 1
         comments = entry.comment.split()
@@ -38,12 +61,11 @@
                     continue
                 n_valid += 1
 
-with open(snakemake.output[0], "w") as fout:
-    print(f"totalReads\t{n_reads}", file = fout)
-    print(f"bxTagCount\t{n_bx}", file = fout)
-    print(f"bxValid\t{n_valid}", file = fout)
-    print(f"bxInvalid\t{n_bx - n_valid}", file = fout)
-    print("A00\t",str(inv_dict["A"]), file = fout)
-    print("C00\t",str(inv_dict["C"]), file = fout)
-    print("B00\t",str(inv_dict["B"]), file = fout)
-    print("D00\t",str(inv_dict["D"]), file = fout)
\ No newline at end of file
+print(f"totalReads\t{n_reads}", file = sys.stdout)
+print(f"bxTagCount\t{n_bx}", file = sys.stdout)
+print(f"bxValid\t{n_valid}", file = sys.stdout)
+print(f"bxInvalid\t{n_bx - n_valid}", file = sys.stdout)
+print("A00\t",str(inv_dict["A"]), file = sys.stdout)
+print("C00\t",str(inv_dict["C"]), file = sys.stdout)
+print("B00\t",str(inv_dict["B"]), file = sys.stdout)
+print("D00\t",str(inv_dict["D"]), file = sys.stdout)
diff --git a/src/harpy/scripts/prune_haplotype.py b/src/harpy/bin/prune_haplotype.py
similarity index 100%
rename from src/harpy/scripts/prune_haplotype.py
rename to src/harpy/bin/prune_haplotype.py
diff --git a/src/harpy/preflight.py b/src/harpy/preflight.py
index 07e6bf9cd..5b538b686 100755
--- a/src/harpy/preflight.py
+++ b/src/harpy/preflight.py
@@ -76,7 +76,6 @@ def fastq(inputs, output_dir, threads, snakemake, quiet, hpc, conda, print_only)
     os.makedirs(f"{workflowdir}/", exist_ok= True)
     fqlist, n = parse_fastq_inputs(inputs)
     fetch_rule(workflowdir, "preflight-fastq.smk")
-    fetch_script(workflowdir, "checkFASTQ.py")
     fetch_report(workflowdir, "PreflightFastq.Rmd")
 
     with open(f"{workflowdir}/config.yaml", "w", encoding="utf-8") as config:
@@ -136,7 +135,6 @@ def bam(inputs, output_dir, threads, snakemake, quiet, hpc, conda, print_only):
     bamlist, n = parse_alignment_inputs(inputs)
     fetch_rule(workflowdir, "preflight-bam.smk")
     fetch_report(workflowdir, "PreflightBam.Rmd")
-    fetch_script(workflowdir, "checkBAM.py")
 
     with open(f"{workflowdir}/config.yaml", "w", encoding="utf-8") as config:
         config.write("workflow: preflight bam\n")
diff --git a/src/harpy/qc.py b/src/harpy/qc.py
index 120fedf9f..477b0c31e 100644
--- a/src/harpy/qc.py
+++ b/src/harpy/qc.py
@@ -67,7 +67,6 @@ def qc(inputs, output_dir, min_length, max_length, ignore_adapters, extra_params
 
     os.makedirs(workflowdir, exist_ok=True)
     fqlist, sample_count = parse_fastq_inputs(inputs)
-    fetch_script(workflowdir, "countBX.py")
     fetch_rule(workflowdir, "qc.smk")
     fetch_report(workflowdir, "BxCount.Rmd")
 
diff --git a/src/harpy/snakefiles/align-bwa.smk b/src/harpy/snakefiles/align-bwa.smk
index 3c3617a98..f83acfbf7 100644
--- a/src/harpy/snakefiles/align-bwa.smk
+++ b/src/harpy/snakefiles/align-bwa.smk
@@ -186,12 +186,12 @@ rule assign_molecules:
         bai = outdir + "/{sample}.bam.bai"
     params:
         molecule_distance
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Assigning barcodes to molecules: {wildcards.sample}"
-    script:
-        "scripts/assignMI.py"
+    shell:
+        "assignMI.py -o {output.bam} -c {params} {input.bam}"
 
 rule bxstats:
     input:
@@ -201,12 +201,12 @@ rule bxstats:
         outdir + "/reports/data/bxstats/{sample}.bxstats.gz"
     params:
         sample = lambda wc: d[wc.sample]
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Calculating barcoded alignment statistics: {wildcards.sample}"
-    script:
-        "scripts/bxStats.py"
+    shell:
+        "bxStats.py -o {output} {input.bam}"
 
 rule coverage:
     input: 
diff --git a/src/harpy/snakefiles/align-ema.smk b/src/harpy/snakefiles/align-ema.smk
index ee410dd5c..f95182abf 100644
--- a/src/harpy/snakefiles/align-ema.smk
+++ b/src/harpy/snakefiles/align-ema.smk
@@ -306,12 +306,12 @@ rule bx_stats:
         bai = outdir + "/{sample}.bam.bai"
     output: 
         outdir + "/reports/data/bxstats/{sample}.bxstats.gz"
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Calculating barcode alignment statistics: {wildcards.sample}"
-    script:
-        "scripts/bxStats.py"
+    shell:
+        "bxStats.py -o {output} {input.bam}"
 
 rule report_persample:
     input:
diff --git a/src/harpy/snakefiles/align-strobealign.smk b/src/harpy/snakefiles/align-strobealign.smk
index 6a5bbc331..9d5e45564 100644
--- a/src/harpy/snakefiles/align-strobealign.smk
+++ b/src/harpy/snakefiles/align-strobealign.smk
@@ -185,12 +185,12 @@ rule assign_molecules:
         bai = outdir + "/{sample}.bam.bai"
     params:
         molecule_distance
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Assigning barcodes to molecules: {wildcards.sample}"
-    script:
-        "scripts/assignMI.py"
+    shell:
+        "assignMI.py -o {output.bam} -c {params} {input.bam}"
 
 rule bxstats:
     input:
@@ -200,12 +200,12 @@ rule bxstats:
         outdir + "/reports/data/bxstats/{sample}.bxstats.gz"
     params:
         sample = lambda wc: d[wc.sample]
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Calculating barcode alignment statistics: {wildcards.sample}"
-    script:
-        "scripts/bxStats.py"
+    shell:
+        "bxStats.py -o {output} {input.bam}"
 
 rule coverage:
     input: 
diff --git a/src/harpy/snakefiles/preflight-bam.smk b/src/harpy/snakefiles/preflight-bam.smk
index 64f8979c4..e3a7decd7 100644
--- a/src/harpy/snakefiles/preflight-bam.smk
+++ b/src/harpy/snakefiles/preflight-bam.smk
@@ -78,12 +78,12 @@ rule check_bam:
         bai = get_align_index
     output:
         temp(out_dir + "/{sample}.log")
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Processing: {wildcards.sample}"
-    script: 
-        "scripts/checkBAM.py"
+    shell: 
+        "checkBAM.py {input.bam} > {output}"
 
 rule merge_checks:
     input:
diff --git a/src/harpy/snakefiles/preflight-fastq.smk b/src/harpy/snakefiles/preflight-fastq.smk
index 84fcacb7a..6142fe1cb 100644
--- a/src/harpy/snakefiles/preflight-fastq.smk
+++ b/src/harpy/snakefiles/preflight-fastq.smk
@@ -58,12 +58,12 @@ rule check_forward:
         get_fq1
     output:
         temp(out_dir + "/{sample}.F.log")
-    conda:
-        f"{envdir}/qc.yaml"
+    container:
+        None
     message:
         "Processing forward reads: {wildcards.sample}"
-    script: 
-        "scripts/checkFASTQ.py"
+    shell: 
+        "checkFASTQ.py {input} > {output}"
 
 rule check_reverse:
     input:
@@ -72,10 +72,10 @@ rule check_reverse:
         temp(out_dir + "/{sample}.R.log")
     message:
         "Processing reverse reads: {wildcards.sample}"
-    conda:
-        f"{envdir}/qc.yaml"
-    script: 
-        "scripts/checkFASTQ.py"
+    container:
+        None
+    shell: 
+        "checkFASTQ.py {input} > {output}"
 
 rule merge_checks:
     input:
diff --git a/src/harpy/snakefiles/qc.smk b/src/harpy/snakefiles/qc.smk
index 3621ebee9..16598ea3c 100644
--- a/src/harpy/snakefiles/qc.smk
+++ b/src/harpy/snakefiles/qc.smk
@@ -89,10 +89,10 @@ rule count_beadtags:
         temp(outdir + "/logs/bxcount/{sample}.count.log")
     message:
         "Counting barcode frequency: {wildcards.sample}"
-    conda:
-        f"{envdir}/qc.yaml"
-    script:
-        "scripts/countBX.py"
+    container:
+        None
+    shell:
+        "countBX.py {input} > {output}"
 
 rule beadtag_counts_summary:
     input: