Link rather than mv

modules/nf-core/porechop/porechop/main.nf

@@ -23,10 +23,10 @@ process PORECHOP_PORECHOP {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
-    mv $reads ${prefix}.fastq.gz
+    ln -s $reads ${prefix}.fastq.gz
 
     porechop \\
-        -i $reads \\
+        -i ${prefix}.fastq.gz \\
         -t $task.cpus \\
         $args \\
         -o ${prefix}_porechopped.fastq.gz \\

modules/nf-core/porechop/porechop/porechop-porechop.diff

@@ -6,10 +6,11 @@ Changes in module 'nf-core/porechop/porechop'
      def prefix = task.ext.prefix ?: "${meta.id}"
      """
 +    ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
-+    mv $reads ${prefix}.fastq.gz
++    ln -s $reads ${prefix}.fastq.gz
 +
      porechop \\
-         -i $reads \\
+-        -i $reads \\
++        -i ${prefix}.fastq.gz \\
          -t $task.cpus \\
          $args \\
 -        -o ${prefix}.fastq.gz \\