From afe63e74c2404802db17f579f349420a4a069880 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andri=20Fr=C3=A4nkl?= <andri.fraenkl@unibas.ch>
Date: Mon, 19 Dec 2022 10:15:04 +0000
Subject: [PATCH] Update Trans_Struc_Gen.nf
---
Trans_Struc_Gen.nf | 47 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/Trans_Struc_Gen.nf b/Trans_Struc_Gen.nf
index cda5799..fa30564 100644
--- a/Trans_Struc_Gen.nf
+++ b/Trans_Struc_Gen.nf
@@ -52,3 +52,50 @@ process file_validation {
"""
}
+
+/*
+ * Define the transcript structure generation
+ * Read gtf files to define exons/introns and add random mutation coefficient.
+ */
+
+process struc_gen {
+
+ input:
+
+
+ output:
+
+
+ script:
+ """
+
+
+ """
+}
+
+
+
+/* Start the job:
+ * initialize variables
+ */
+
+Channel
+ .fromFilePairs( params.reads, checkIfExists:true )
+ .set { read_pairs_ch }
+
+
+/* The "main" function:
+ * Use CLI arguments to create structure sequences and output text file & gtf file with selected exon structures
+ */
+
+workflow {
+ file_validation_ch = file_validation(params.cvs_file, params.gtf_file)
+ struc_gen_ch = struc_gen( # No idea yet) }
+
+
+/* Book keeping upon workflow completion */
+workflow.onComplete {
+ log.info (workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc/multiqc_report.html\n" : "Oops .. something went wrong")
+ )
+}
+```
--
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