diff --git a/modules/nf-core/seqkit/sample/main.nf b/modules/nf-core/seqkit/sample/main.nf
index 96ddc814db46..6b235e42ec29 100644
--- a/modules/nf-core/seqkit/sample/main.nf
+++ b/modules/nf-core/seqkit/sample/main.nf
@@ -11,7 +11,7 @@ process SEQKIT_SAMPLE {
     tuple val(meta), path(fastx)
 
     output:
-    tuple val(meta), path("${prefix}.${extension}"), emit: fastx
+    tuple val(meta), path("${prefix}*.${extension}"), emit: fastx
     tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions
 
     when:
@@ -20,35 +20,62 @@ process SEQKIT_SAMPLE {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    def fastx_list = fastx instanceof List ? fastx : [fastx]
+    def first_file = fastx_list[0].toString()
     extension = "fastq"
-    if ("${fastx}" ==~ /.+\.(fasta|fa|fas|fna|fsa)(\.gz)?/) {
+    if (first_file ==~ /.+\.(fasta|fa|fas|fna|fsa)(\.gz)?/) {
         extension = "fasta"
     }
-    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    if ("${prefix}.${extension}" == "${fastx}") {
-        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    extension = first_file.endsWith('.gz') ? "${extension}.gz" : extension
+
+    def cmds = []
+    if (fastx_list.size() == 1) {
+        def out_name = "${prefix}.${extension}"
+        if (out_name == "${fastx_list[0]}") {
+            error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+        }
+        cmds << "seqkit sample --threads ${task.cpus} ${args} ${fastx_list[0]} -o ${out_name}"
+    } else {
+        fastx_list.eachWithIndex { f, i ->
+            def out_name = "${prefix}_${i + 1}.${extension}"
+            if (out_name == "${f}") {
+                error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+            }
+            cmds << "seqkit sample --threads ${task.cpus} ${args} ${f} -o ${out_name}"
+        }
     }
     """
-    seqkit \\
-        sample \\
-        --threads ${task.cpus} \\
-        ${args} \\
-        ${fastx} \\
-        -o ${prefix}.${extension}
+    ${cmds.join(' \\\n    && ')}
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
+    def fastx_list = fastx instanceof List ? fastx : [fastx]
+    def first_file = fastx_list[0].toString()
     extension = "fastq"
-    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta\.gz|.+\.fa|.+\.fa\.gz|.+\.fas|.+\.fas\.gz|.+\.fna|.+\.fna\.gz|.+\.fsa|.+\.fsa\.gz/) {
+    if (first_file ==~ /.+\.(fasta|fa|fas|fna|fsa)(\.gz)?/) {
         extension = "fasta"
     }
-    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    if ("${prefix}.${extension}" == "${fastx}") {
-        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
-    }
+    extension = first_file.endsWith('.gz') ? "${extension}.gz" : extension
     def create_cmd = extension.endsWith('.gz') ? "echo '' | gzip >" : "touch"
+
+    def stub_cmds = []
+    if (fastx_list.size() == 1) {
+        def out_name = "${prefix}.${extension}"
+        if (out_name == "${fastx_list[0]}") {
+            error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+        }
+        stub_cmds << "${create_cmd} ${out_name}"
+    } else {
+        fastx_list.eachWithIndex { f, i ->
+            def out_name = "${prefix}_${i + 1}.${extension}"
+            if (out_name == "${f}") {
+                error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+            }
+            stub_cmds << "${create_cmd} ${out_name}"
+        }
+    }
     """
-    ${create_cmd} ${prefix}.${extension}
+    ${stub_cmds.join('\n    ')}
     """
 }