diff --git a/.test/config/config.yml b/.test/config/config.yml
index 5cccf41..9d023d4 100644
--- a/.test/config/config.yml
+++ b/.test/config/config.yml
@@ -60,7 +60,7 @@ mapping_stats:
     genome_size: 1000
     extra: ""
   deeptools_plotcoverage:
-    extra: ""
+    extra: "--numberOfSamples 10000 --skipZeros --coverageThresholds 1"
 
 variant_calling:
   tool: "freebayes"
diff --git a/config/config.yml b/config/config.yml
index 5cccf41..9d023d4 100644
--- a/config/config.yml
+++ b/config/config.yml
@@ -60,7 +60,7 @@ mapping_stats:
     genome_size: 1000
     extra: ""
   deeptools_plotcoverage:
-    extra: ""
+    extra: "--numberOfSamples 10000 --skipZeros --coverageThresholds 1"
 
 variant_calling:
   tool: "freebayes"
diff --git a/config/schemas/config.schema.yml b/config/schemas/config.schema.yml
index f74ca60..aa96695 100644
--- a/config/schemas/config.schema.yml
+++ b/config/schemas/config.schema.yml
@@ -169,11 +169,13 @@ properties:
           extra:
             type: string
             description: additional arguments to pass to DeepTools plotCoverage
+            default: "--numberOfSamples 10000 --skipZeros --coverageThresholds 1"
     required:
       - gffread
       - rseqc_infer_experiment
       - rseqc_bam_stat
       - deeptools_coverage
+      - deeptools_plotcoverage
   variant_calling:
     type: object
     properties:
diff --git a/workflow/rules/bowtie2.smk b/workflow/rules/bowtie2.smk
index 5972de6..8192da9 100644
--- a/workflow/rules/bowtie2.smk
+++ b/workflow/rules/bowtie2.smk
@@ -25,8 +25,9 @@ rule bowtie2_build:
 rule bowtie2_align:
     input:
         sample=expand(
-            "results/fastp/{{sample}}_{read}.fastq.gz",
+            "results/{tool}/{{sample}}_{read}.fastq.gz",
             read=["read1", "read2"] if is_paired_end() else ["read1"],
+            tool=config["processing"]["tool"],
         ),
         idx=rules.bowtie2_build.output,
     output:
diff --git a/workflow/rules/bwamem2.smk b/workflow/rules/bwamem2.smk
index 178e930..3e28efe 100644
--- a/workflow/rules/bwamem2.smk
+++ b/workflow/rules/bwamem2.smk
@@ -21,8 +21,9 @@ rule bwa_mem2_index:
 rule bwa_mem2:
     input:
         reads=expand(
-            "results/fastp/{{sample}}_{read}.fastq.gz",
+            "results/{tool}/{{sample}}_{read}.fastq.gz",
             read=["read1", "read2"] if is_paired_end() else ["read1"],
+            tool=config["processing"]["tool"],
         ),
         idx=rules.bwa_mem2_index.output,
     output:
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index bed5b41..e80dc8d 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -1,6 +1,7 @@
 # import basic packages
 import pandas as pd
 from snakemake.utils import validate
+from snakemake.logging import logger
 from pathlib import Path
 
 # read sample sheet
@@ -86,8 +87,9 @@ def get_multiqc_input(wildcards):
         tool=config["mapping"]["tool"],
     )
     result += expand(
-        "results/fastp/{sample}.json",
+        "results/{tool}/{sample}.json",
         sample=samples.index,
+        tool=config["processing"]["tool"],
     )
     result += expand(
         "results/rseqc/{tool}/{sample}.txt",
@@ -120,3 +122,21 @@ def get_multiqc_input(wildcards):
         ),
     )
     return result
+
+
+# stop workflow when paired-end reads are used as input for fastplong
+if is_paired_end() and config["processing"]["tool"] == "fastplong":
+    config["processing"]["tool"] = "fastp"
+    logger.warning(
+        "\nWARNING: fastplong cannot be used with paired-end reads in this workflow.\n"
+        + "Fastp will be used as a replacement.\n"
+        + "Please consult the fastplong documentation for details.\n"
+    )
+
+# trigger warning when paired-end reads are used with minimap2
+if is_paired_end() and config["mapping"]["tool"] == "minimap2":
+    logger.warning(
+        "\nWARNING: minimap2 is being used with paired-end reads.\n"
+        + "This is possible but may require additional parameters to run.\n"
+        + "Please consult the minimap2 documentation for details.\n"
+    )
diff --git a/workflow/rules/mapping_stats.smk b/workflow/rules/mapping_stats.smk
index aadb6f5..0b299fe 100644
--- a/workflow/rules/mapping_stats.smk
+++ b/workflow/rules/mapping_stats.smk
@@ -111,6 +111,6 @@ rule deeptools_plotcoverage:
         "results/deeptools/coverage/{sample}_coverage.log",
     threads: 4
     params:
-        extra="--coverageThresholds 1",
+        extra=config["mapping_stats"]["deeptools_plotcoverage"]["extra"],
     wrapper:
         "v5.6.0/bio/deeptools/plotcoverage"
diff --git a/workflow/rules/minimap2.smk b/workflow/rules/minimap2.smk
index 8316612..4b0c05e 100644
--- a/workflow/rules/minimap2.smk
+++ b/workflow/rules/minimap2.smk
@@ -16,8 +16,9 @@ rule minimap2_align:
     input:
         target=rules.minimap2_index.output.index,
         query=expand(
-            "results/fastp/{{sample}}_{read}.fastq.gz",
+            "results/{tool}/{{sample}}_{read}.fastq.gz",
             read=["read1", "read2"] if is_paired_end() else ["read1"],
+            tool=config["processing"]["tool"],
         ),
     output:
         "results/minimap2/align/{sample}/mapped.bam",
diff --git a/workflow/rules/star.smk b/workflow/rules/star.smk
index bd74482..0c38f5a 100644
--- a/workflow/rules/star.smk
+++ b/workflow/rules/star.smk
@@ -16,8 +16,18 @@ rule star_index:
 
 rule star_align:
     input:
-        fq1="results/fastp/{sample}_read1.fastq.gz",
-        fq2="results/fastp/{sample}_read2.fastq.gz" if is_paired_end() else [],
+        fq1=expand(
+            "results/{tool}/{{sample}}_read1.fastq.gz",
+            tool=config["processing"]["tool"],
+        ),
+        fq2=(
+            expand(
+                "results/{tool}/{{sample}}_read2.fastq.gz",
+                tool=config["processing"]["tool"],
+            )
+            if is_paired_end()
+            else []
+        ),
         idx=rules.star_index.output,
     output:
         aln="results/star/align/{sample}/mapped.bam",