diff --git a/modules/nf-core/mitohifi/mitohifi/environment.yml b/modules/nf-core/mitohifi/mitohifi/environment.yml
deleted file mode 100644
index bcd3a8b1c632..000000000000
--- a/modules/nf-core/mitohifi/mitohifi/environment.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
diff --git a/modules/nf-core/mitohifi/mitohifi/main.nf b/modules/nf-core/mitohifi/mitohifi/main.nf
index de9b3fd39b0e..7f2bc2a058af 100644
--- a/modules/nf-core/mitohifi/mitohifi/main.nf
+++ b/modules/nf-core/mitohifi/mitohifi/main.nf
@@ -10,6 +10,7 @@ process MITOHIFI_MITOHIFI {
     tuple val(meta), path(input)
     path ref_fa
     path ref_gb
+    val input_mode
     val mito_code
 
     output:
@@ -41,13 +42,11 @@ process MITOHIFI_MITOHIFI {
     }
 
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
-    if (! ["-c", "-r"].contains(args2)) {
-        error "-r for reads or -c for contigs must be specified"
+    if (! ["c", "r"].contains(input_mode)) {
+        error "r for reads or c for contigs must be specified"
     }
-    def script_input = "${args2} ${input}"
     """
-    mitohifi.py ${script_input} \\
+    mitohifi.py -${input_mode} ${input} \\
         -f ${ref_fa} \\
         -g ${ref_gb} \\
         -o ${mito_code} \\
diff --git a/modules/nf-core/mitohifi/mitohifi/meta.yml b/modules/nf-core/mitohifi/mitohifi/meta.yml
index a4f1658a3b3e..bd80dc27234a 100644
--- a/modules/nf-core/mitohifi/mitohifi/meta.yml
+++ b/modules/nf-core/mitohifi/mitohifi/meta.yml
@@ -25,6 +25,10 @@ input:
       type: file
       description: Reference annotation
       pattern: "*.{gb}"
+  - input_mode:
+      type: string
+      description: Specifies type of input - reads or contigs
+      pattern: "{r,c}"
   - code:
       type: integer
       description: Mitochndrial code for annotation
diff --git a/tests/modules/nf-core/mitohifi/mitohifi/main.nf b/tests/modules/nf-core/mitohifi/mitohifi/main.nf
index afbc5759848d..f5a0a95c6b76 100644
--- a/tests/modules/nf-core/mitohifi/mitohifi/main.nf
+++ b/tests/modules/nf-core/mitohifi/mitohifi/main.nf
@@ -12,8 +12,9 @@ workflow test_mitohifi_mitohifi_contigs {
     data_contigs = Channel.of([[id:"ilDeiPorc1"],file(params.test_data['deilephila_porcellus']['mito']['contigs'], checkIfExists: true)])
     ref_gb = file(params.test_data['deilephila_porcellus']['mito']['ref_gb'], checkIfExists: true)
     ref_fa = file(params.test_data['deilephila_porcellus']['mito']['ref_fa'], checkIfExists: true)
+    input_mode = Channel.of('c')
     code = 5
-    MITOHIFI_MITOHIFI_CONTIGS ( data_contigs, ref_fa, ref_gb, code )
+    MITOHIFI_MITOHIFI_CONTIGS ( data_contigs, ref_fa, ref_gb, input_mode, code )
 }
 
 
@@ -24,6 +25,7 @@ workflow test_mitohifi_mitohifi_reads {
     data_reads = Channel.of([[id:"ilDeiPorc1"],file(params.test_data['deilephila_porcellus']['mito']['hifi_reads'], checkIfExists: true)])
     ref_gb = file(params.test_data['deilephila_porcellus']['mito']['ref_gb'], checkIfExists: true)
     ref_fa = file(params.test_data['deilephila_porcellus']['mito']['ref_fa'], checkIfExists: true)
+    input_mode = Channel.of('r')
     code = 5
-    MITOHIFI_MITOHIFI_READS ( data_reads, ref_fa, ref_gb, code )
+    MITOHIFI_MITOHIFI_READS ( data_reads, ref_fa, ref_gb, input_mode, code )
 }
diff --git a/tests/modules/nf-core/mitohifi/mitohifi/nextflow.config b/tests/modules/nf-core/mitohifi/mitohifi/nextflow.config
index b0144acc668b..94a611a79f74 100644
--- a/tests/modules/nf-core/mitohifi/mitohifi/nextflow.config
+++ b/tests/modules/nf-core/mitohifi/mitohifi/nextflow.config
@@ -1,11 +1,5 @@
 process {
-    withName: MITOHIFI_MITOHIFI_CONTIGS {
-        ext.args2 = '-c'
-        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    }
-
-    withName: MITOHIFI_MITOHIFI_READS {
-        ext.args2 = '-r'
+    withName: MITOHIFI_MITOHIFI {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     }
 }