From a1172ba92878602b17133208048a0301c719a2cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andri=20Fr=C3=A4nkl?= <andri.fraenkl@unibas.ch>
Date: Fri, 16 Dec 2022 09:26:17 +0000
Subject: [PATCH] Add new file
---
Trans_Struc_Gen.nf | 54 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 Trans_Struc_Gen.nf
diff --git a/Trans_Struc_Gen.nf b/Trans_Struc_Gen.nf
new file mode 100644
index 0000000..cda5799
--- /dev/null
+++ b/Trans_Struc_Gen.nf
@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+```c
+/*
+ * Define the input parameters"""Takes input from csv-formatted file ("ID,Count")
+ with counts for individual transcripts.
+ Also a gtf-formatted file with exon coordinates
+ of the transcripts included in the csv file.
+ Outputs gtf-formatted file containing
+ generated intron/exon structures per transcript.
+ Outputs csv-formatted file
+ ("NewTranscriptID,ID,Count") with id of
+ generated transcript, id of original
+ transcript (without intron inclusions) and
+ Counts.
+ */
+params.cvs_file = "$projectDir/tests/ #Input cvs file from group 1
+params.gtf_file = "$projectDir/tests/ #Input gtf file from group 1
+params.outdir = "results"
+
+
+/* Log some information for the user */
+
+log.info """\
+ R N A S E Q - N F P I P E L I N E
+ ===================================
+ cvs_file : ${params.cvs_file}
+ gtf_file : ${params.gtf_file}
+ outdir : ${params.outdir}
+ """
+ .stripIndent()
+
+/*
+ * define the `file_validation` process
+ * given that the input files exist and are the correct format
+ */
+
+process file_validation {
+
+ input:
+ path cvs_file
+ path gtf_file
+
+ output:
+ path cvs_file into struc_gen
+ path gtf_file into struc_gen
+
+ script:
+ """
+
+ """
+}
--
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