From 39039620be825a5ec8429e1a7cc7da33719893a0 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Wed, 27 Sep 2023 12:21:05 +0100
Subject: [PATCH 1/2] Update main.nf to include stub

Adding the stub for SeqKit Sliding
---
 modules/nf-core/seqkit/sliding/main.nf | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/modules/nf-core/seqkit/sliding/main.nf b/modules/nf-core/seqkit/sliding/main.nf
index ffa570eb58f..d2a7a90f59d 100644
--- a/modules/nf-core/seqkit/sliding/main.nf
+++ b/modules/nf-core/seqkit/sliding/main.nf
@@ -37,4 +37,17 @@ process SEQKIT_SLIDING {
         seqkit: \$( seqkit | sed '3!d; s/Version: //' )
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fastx" ==~ /.+\.fasta$|.+\.fa$|.+\.fas$|.+\.fna$/) {
+        extension = "fasta"
+    }    """
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """
 }

From 9901533c4ac97b60d9ed6b2ad37701a101478aa4 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Thu, 28 Sep 2023 10:19:50 +0100
Subject: [PATCH 2/2] Review fix

---
 modules/nf-core/seqkit/sliding/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/seqkit/sliding/main.nf b/modules/nf-core/seqkit/sliding/main.nf
index d2a7a90f59d..0f385c68cef 100644
--- a/modules/nf-core/seqkit/sliding/main.nf
+++ b/modules/nf-core/seqkit/sliding/main.nf
@@ -42,7 +42,8 @@ process SEQKIT_SLIDING {
     prefix = task.ext.prefix ?: "${meta.id}"
     if ("$fastx" ==~ /.+\.fasta$|.+\.fa$|.+\.fas$|.+\.fna$/) {
         extension = "fasta"
-    }    """
+    }
+    """
     touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml