diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf
index fc027793..7e361a06 100644
--- a/modules/seqkit/split2/main.nf
+++ b/modules/seqkit/split2/main.nf
@@ -2,29 +2,30 @@ process SEQKIT_SPLIT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
+    conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0' :
-        'quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
+        'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*${prefix}/*.gz"), emit: reads
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("**/*.gz"), emit: reads
+    path "versions.yml"             , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     if(meta.single_end){
         """
         seqkit \\
             split2 \\
             $args \\
             --threads $task.cpus \\
-            -1 $reads \\
-            --out-dir $prefix
+            $reads \\
+            --out-dir ${prefix}
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -37,9 +38,9 @@ process SEQKIT_SPLIT2 {
             split2 \\
             $args \\
             --threads $task.cpus \\
-            -1 ${reads[0]} \\
-            -2 ${reads[1]} \\
-            --out-dir $prefix
+            --read1 ${reads[0]} \\
+            --read2 ${reads[1]} \\
+            --out-dir ${prefix}
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
diff --git a/tests/modules/seqkit/split2/test.yml b/tests/modules/seqkit/split2/test.yml
index 12b02072..00368e22 100644
--- a/tests/modules/seqkit/split2/test.yml
+++ b/tests/modules/seqkit/split2/test.yml
@@ -1,83 +1,95 @@
-- name: seqkit split2 single-end length
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_single_end_length
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
+      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: cf38c51506e45380fe25abdd1bd5ccc6
+      md5sum: 45cccacb4676bca33beb17064322a781
+    - path: output/seqkit/versions.yml
+      md5sum: 2d5a709d129be364687cc0b561efa532
 
-- name: seqkit split2 single-end size
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_single_end_size
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: bf835e685d597fc1ab5e5ac7dd689619
+      md5sum: b09324606fb3636b51448d6a007d2c71
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
+      md5sum: f7873475d463e3b4d21dccbf8e859270
+    - path: output/seqkit/versions.yml
+      md5sum: 490d00accd1092a8eca4e83ed809bad3
 
-- name: seqkit split2 single-end part
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_single_end_part
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: fa25951435471238d5567fd2cae31f55
+      md5sum: a9d29d08e27246b6d36e21e5def405e3
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
+      md5sum: 6d547a959adcd027dd1a8734e195dd7d
     - path: output/seqkit/test/test_1.part_003.fastq.gz
-      md5sum: 8bc86ba83a611c54f592f4eae19b680f
+      md5sum: 6d63cc8400dd2a96d808514fb18278ee
+    - path: output/seqkit/versions.yml
+      md5sum: 90431cd3d28954f656988230d4481115
 
-- name: seqkit split2 paired-end length
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_paired_end_length
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
+      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: cf38c51506e45380fe25abdd1bd5ccc6
+      md5sum: 45cccacb4676bca33beb17064322a781
     - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4
+      md5sum: 160b5fd363ff7cad8af9d914269d6426
     - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 927097c6ac7522199a9e016333181a8e
+      md5sum: 18bc5434cf55706394cccb44e6108561
+    - path: output/seqkit/versions.yml
+      md5sum: 9272afc1a126ae997a712edeef317f22
 
-- name: seqkit split2 paired-end size
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_paired_end_size
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: bf835e685d597fc1ab5e5ac7dd689619
+      md5sum: b09324606fb3636b51448d6a007d2c71
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
+      md5sum: f7873475d463e3b4d21dccbf8e859270
     - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba
+      md5sum: c0602b62aae860dd284c0eb0062c24dd
     - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 8796c3f327b1094244bfcdb36d536526
+      md5sum: 5bc7a98b618100b29910eb41c4c9ac0d
+    - path: output/seqkit/versions.yml
+      md5sum: af66912ae8abc493f77f70e3bf473144
 
-- name: seqkit split2 paired-end part
-  command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
+- name: seqkit split2 test_seqkit_split2_paired_end_part
+  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
   files:
     - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: fa25951435471238d5567fd2cae31f55
+      md5sum: a9d29d08e27246b6d36e21e5def405e3
     - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
+      md5sum: 6d547a959adcd027dd1a8734e195dd7d
     - path: output/seqkit/test/test_1.part_003.fastq.gz
-      md5sum: 8bc86ba83a611c54f592f4eae19b680f
+      md5sum: 6d63cc8400dd2a96d808514fb18278ee
     - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: f0055c99cd193fd97466b3cde9dd1b8f
+      md5sum: b51a1bed106e4ec0c9be7d9e224d0616
     - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 8a90df768201785f7a7cd5dbb41e846a
+      md5sum: 079078a7f86114ae29cda8c00d5a7fc9
     - path: output/seqkit/test/test_2.part_003.fastq.gz
-      md5sum: 890b90083e8e1606bd13ba34149cedd7
+      md5sum: 6987941bf8c4a37565e333029ba41ca0
+    - path: output/seqkit/versions.yml
+      md5sum: 193bc5f0c429076f816ab0a529c4c1fc