From 973a4b0d6e2f18817fa00343715e57a935cef586 Mon Sep 17 00:00:00 2001
From: gwajnberg <gabriel.wajnberg@hotmail.com>
Date: Wed, 12 Apr 2023 14:37:23 -0600
Subject: [PATCH] Create filtering.nf

---
 subworkflow/filtering.nf | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 subworkflow/filtering.nf

diff --git a/subworkflow/filtering.nf b/subworkflow/filtering.nf
new file mode 100644
index 0000000..4921f1a
--- /dev/null
+++ b/subworkflow/filtering.nf
@@ -0,0 +1,21 @@
+process FILTERING {
+
+    input:
+        val(datadir)
+        val(publishdir)
+        val(target)
+        val(length)
+        val(qcscore)
+
+    output:
+        val(datadir)
+
+    script:
+
+        """
+        fastqc -o ${publishdir} ${datadir}/${target}/${target}.fastq.gz
+        gunzip -c ${datadir}.fastq.gz| chopper -q ${qcscore} --minlength ${length} -t 30 | gzip > ${publishdir}/${datadir}_filtered.fastq.gz
+        fastqc -o ${publishdir} ${publishdir}/${datadir}_filtered.fastq.gz
+        """
+
+}