diff --git a/.tests/config/config.yaml b/.tests/config/config.yaml
index 25a8ea6f4..affb3f1a5 100644
--- a/.tests/config/config.yaml
+++ b/.tests/config/config.yaml
@@ -77,7 +77,9 @@ preprocessing:
   # for more information
   artic-primer-version: 3
   # path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
-  amplicon-primers: "resources/nCoV-2019.primer.bed"
+  amplicon-primers: 
+    ont: "resources/nCoV-2019.primer.bed"
+    illumina: "resources/nCoV-2019.primer.bed"
   # GenBank accession of reference sequence of the amplicon primers
   amplicon-reference: "MN908947"
 
diff --git a/config/config.yaml b/config/config.yaml
index 898b305ac..97d3a33c0 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -63,7 +63,9 @@ preprocessing:
   # for more information
   artic-primer-version: 3
   # path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
-  amplicon-primers: "resources/nCoV-2019.primer.bed"
+  amplicon-primers: 
+    ont: "resources/nCoV-2019.primer.bed"
+    illumina: "resources/nCoV-2019.primer.bed"
   # GenBank accession of reference sequence of the amplicon primers
   amplicon-reference: "MN908947"
 
diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index 33e4cec03..83f6c994a 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -56,7 +56,7 @@ rule nanofilt:
 
 rule downsample_and_trim_raw:
     input:
-        primer=config["preprocessing"]["amplicon-primers"],
+        primer=config["preprocessing"]["amplicon-primers"]["ont"],
         reads="results/{date}/filtered/nanofilt/{sample}.fastq",
         ref_genome="resources/genomes/main.fasta",
     output:
@@ -121,7 +121,7 @@ rule canu_correct:
 
 rule clip_adbc_corrected:
     input:
-        primer=config["preprocessing"]["amplicon-primers"],
+        primer=config["preprocessing"]["amplicon-primers"]["ont"],
         reads="results/{date}/corrected/{sample}/{sample}.correctedReads.fasta",
         ref_genome="resources/genomes/main.fasta",
     output:
diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
index 8d93acc74..c759c5e05 100644
--- a/workflow/rules/read_clipping.smk
+++ b/workflow/rules/read_clipping.smk
@@ -22,7 +22,7 @@ rule samtools_sort:
 
 rule bed_to_bedpe:
     input:
-        check_bed_for_URL(config["preprocessing"]["amplicon-primers"]),
+        check_bed_for_URL(config["preprocessing"]["amplicon-primers"]["illumina"]),
     output:
         "resources/primer.bedpe",
     log:
diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
index d4d498813..b0d0278ac 100644
--- a/workflow/schemas/config.schema.yaml
+++ b/workflow/schemas/config.schema.yaml
@@ -67,8 +67,14 @@ properties:
         type: integer
         description: only for Oxford Nanopore data. ARTIC primer version to clip from reads
       amplicon-primers:
-        type: string
-        description: path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
+        type: object
+        properties:
+          ont:
+            type: string
+            description: path to amplicon primers in bed format for hard-clipping on single end files (Oxford Nanopore)
+          illumina:
+            type: string
+            description: path to amplicon primers in bed format for hard-clipping on paired end files (Illumina)
       amplicon-reference:
         type: string
         description: GenBank accession of reference sequence of the amplicon primers