diff --git a/zamp/rules/5_visualization/QIIME2_import.rules b/zamp/rules/5_visualization/QIIME2_import.rules
index 03651ed..72b46a3 100644
--- a/zamp/rules/5_visualization/QIIME2_import.rules
+++ b/zamp/rules/5_visualization/QIIME2_import.rules
@@ -1,29 +1,29 @@
 rule create_biom_from_count_table:
     conda:
-        "../../envs/amplicons_r_utils.yml"
+        os.path.join(dir.envs, "amplicons_r_utils.yml")
     container:
         singularity_envs["r_utils"]
     input:
-        count_table="{prefix}/count_table.tsv",
+        count_table=os.path.join(dir.out.base, "{prefix}", "count_table.tsv"),
     output:
-        biom_count="{prefix}/otu_biom.biom",
+        biom_count=os.path.join(dir.out.base, "{prefix}", "otu_biom.biom"),
     log:
-        logging_folder + "{prefix}/otu_biom.txt",
+        os.path.join(dir.logs, "{prefix}", "otu_biom.txt"),
     script:
         "scripts/create_biom_from_count_table.R"
 
 
 rule import_count_table_to_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{prefix}/otu_biom.biom",
+        os.path.join(dir.out.base, "{prefix}", "otu_biom.biom"),
     output:
-        "{prefix}/count-table.qza",
+        os.path.join(dir.out.base, "{prefix}", "count-table.qza"),
     log:
-        logging_folder + "{prefix}/count-table.txt",
+        os.path.join(dir.logs, "{prefix}", "count-table.txt"),
     shell:
         """
         qiime tools import \
@@ -36,15 +36,15 @@ rule import_count_table_to_QIIME2:
 
 rule create_visualize_count_table_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{prefix}/count-table.qza",
+        os.path.join(dir.out.base, "{prefix}", "count-table.qza"),
     output:
-        "{prefix}/count-table.qzv",
+        os.path.join(dir.out.base, "{prefix}", "count-table.qzv"),
     log:
-        logging_folder + "{prefix}.txt",
+        os.path.join(dir.logs, "{prefix}.txt"),
     shell:
         """
         qiime feature-table summarize \
@@ -55,11 +55,15 @@ rule create_visualize_count_table_QIIME2:
 
 rule force_all_upper_case_rep_seq:
     input:
-        rep_seqs="{denoiser}/{prefix}/dna-sequences.fasta",
+        rep_seqs=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "dna-sequences.fasta"
+        ),
     output:
-        rep_seqs="{denoiser}/{prefix}/dna-sequences_all_UPPER.fasta",
+        rep_seqs=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.fasta"
+        ),
     log:
-        logging_folder + "{denoiser}/{prefix}/dna-sequences_all_UPPER.txt",
+        os.path.join(dir.logs, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.txt"),
     shell:
         """
         awk '/^>/ {{print($0)}}; /^[^>]/ {{print(toupper($0))}}' {input[0]} > {output[0]}
@@ -68,15 +72,17 @@ rule force_all_upper_case_rep_seq:
 
 rule import_rep_seq_to_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        rep_seqs="{denoiser}/{prefix}/dna-sequences_all_UPPER.fasta",
+        rep_seqs=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.fasta"
+        ),
     output:
-        "{denoiser}/{prefix}/rep-seqs.qza",
+        os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rep-seqs.qza"),
     log:
-        logging_folder + "{denoiser}/{prefix}/rep-seqs.txt",
+        os.path.join(dir.logs, "{denoiser}", "{prefix}", "rep-seqs.txt"),
     shell:
         """
         qiime tools import \
@@ -89,18 +95,24 @@ rule import_rep_seq_to_QIIME2:
 # Build a new tree based on the filtered sequences
 rule create_tree_in_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{denoiser}/{prefix}/rep-seqs.qza",
+        os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rep-seqs.qza"),
     output:
-        aligned="{denoiser}/{prefix}/aligned-rep-seqs.qza",
-        masked="{denoiser}/{prefix}/masked-aligned-rep-seqs.qza",
-        unrooted="{denoiser}/{prefix}/unrooted-tree.qza",
-        rooted="{denoiser}/{prefix}/rooted-tree.qza",
+        aligned=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "aligned-rep-seqs.qza"
+        ),
+        masked=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "masked-aligned-rep-seqs.qza"
+        ),
+        unrooted=os.path.join(
+            dir.out.base, "{denoiser}", "{prefix}", "unrooted-tree.qza"
+        ),
+        rooted=os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rooted-tree.qza"),
     log:
-        logging_folder + "{denoiser}/{prefix}/rooted-tree.txt",
+        os.path.join(dir.logs, "{denoiser}", "{prefix}", "rooted-tree.txt"),
     threads: 4
     shell:
         """
@@ -116,15 +128,15 @@ rule create_tree_in_QIIME2:
 
 rule export_QIIME2_tree:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        rooted="{denoiser}/{prefix}/rooted-tree.qza",
+        os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rooted-tree.qza"),
     output:
-        rooted="{denoiser}/{prefix}/tree.nwk",
+        os.path.join(dir.out.base, "{denoiser}", "{prefix}", "tree.nwk"),
     log:
-        logging_folder + "{denoiser}/{prefix}/tree.txt",
+        os.path.join(dir.logs, "{denoiser}", "{prefix}", "tree.txt"),
     shell:
         """
         qiime tools export --input-path {input} --output-path $(dirname {output[0]})
@@ -133,15 +145,15 @@ rule export_QIIME2_tree:
 
 rule create_visualize_rep_seq_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{denoiser}/2_denoised/rep-seqs.qza",
+        os.path.join(dir.out.base, "{denoiser}", "2_denoised", "rep-seqs.qza"),
     output:
-        "{denoiser}/2_denoised/rep-seqs.qzv",
+        os.path.join(dir.out.base, "{denoiser}", "2_denoised", "rep-seqs.qzv"),
     log:
-        logging_folder + "{denoiser}/2_denoised/rep-seqs_qzv.txt",
+        os.path.join(dir.logs, "{denoiser}", "2_denoised", "rep-seqs_qzv.txt"),
     shell:
         """
         qiime feature-table tabulate-seqs \
@@ -152,16 +164,33 @@ rule create_visualize_rep_seq_QIIME2:
 
 rule import_taxonomy_to_Qiime2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
+        os.path.join(
+            dir.out.base,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.txt",
+        ),
     output:
-        "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qza",
+        os.path.join(
+            dir.out.base,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.qza",
+        ),
     log:
-        logging_folder
-        + "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
+        os.path.join(
+            dir.logs,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.txt",
+        ),
     shell:
         """
         qiime tools import \
@@ -174,16 +203,33 @@ rule import_taxonomy_to_Qiime2:
 
 rule create_visualize_table_QIIME2:
     conda:
-        "../../envs/QIIME2-2020.02.yml"
+        os.path.join(dir.envs, "QIIME2-2020.02.yml")
     container:
         singularity_envs["qiime2"]
     input:
-        "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qza",
+        os.path.join(
+            dir.out.base,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.qza",
+        ),
     output:
-        "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qzv",
+        os.path.join(
+            dir.out.base,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.qzv",
+        ),
     log:
-        logging_folder
-        + "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
+        os.path.join(
+            dir.logs,
+            "{denoiser}",
+            "3_classified",
+            "{classifier}_{tax_DB}",
+            "dna-sequences_tax_assignments.txt",
+        ),
     shell:
         """
         qiime metadata tabulate \