refactor: Move NANOFILT module to its own file

main.nf

@@ -2,6 +2,7 @@
 
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
+include { NANOFILT } form './modules/nanofilt'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -69,34 +70,6 @@ workflow {
     )
 }
 
-process NANOFILT {
-    cpus 1
-    memory '8.GB'
-    container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
-
-    input:
-    tuple val(prefix), path(reads)
-
-    output:
-    tuple val(prefix), path("*_trimmed.fastq.gz")
-
-    script:
-    """
-    gzip \\
-            -cdf "${reads}" \\
-        | NanoFilt \\
-            --logfile "trimmed/${prefix}.nanofilt.log" \\
-            --length 100 \\
-            --quality 7 \\
-            --headcrop 30 \\
-            --tailcrop 30 \\
-            --minGC 0.1 \\
-            --maxGC 0.9 \\
-        | gzip \\
-        > "${prefix}_trimmed.fastq.gz"
-    """
-}
-
 process MINIMAP2 {
     cpus 4
     memory '8.GB'

modules/nanofilt/main.nf

@@ -0,0 +1,27 @@
+process NANOFILT {
+    cpus 1
+    memory '8.GB'
+    container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
+
+    input:
+    tuple val(prefix), path(reads)
+
+    output:
+    tuple val(prefix), path("*_trimmed.fastq.gz")
+
+    script:
+    """
+    gzip \\
+            -cdf "${reads}" \\
+        | NanoFilt \\
+            --logfile "trimmed/${prefix}.nanofilt.log" \\
+            --length 100 \\
+            --quality 7 \\
+            --headcrop 30 \\
+            --tailcrop 30 \\
+            --minGC 0.1 \\
+            --maxGC 0.9 \\
+        | gzip \\
+        > "${prefix}_trimmed.fastq.gz"
+    """
+}