From 97daa8b7e452addbccdf69cd2c245b7561075e4b Mon Sep 17 00:00:00 2001
From: chbk <chbk.git@gmail.com>
Date: Wed, 9 Jun 2021 09:05:26 +0200
Subject: [PATCH] Fix novel gene and transcript counts in report

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 0f91bb9..97083e9 100644
--- a/main.nf
+++ b/main.nf
@@ -1258,9 +1258,9 @@ process control_elements {
             transcript_cdna_length_and_TSStorefgeneTSS_distance_for_exact_transcripts.png
 
     reference_genes=\$(awk 'NR == 3 {print \$2}' detected_transcripts_genes_numbers.tsv)
-    novel_genes=\$(awk 'NR == 3 {print \$2 + \$7}' detected_transcripts_genes_numbers.tsv)
+    novel_genes=\$(wc -l string/novel_gnid_nbtr.txt | awk '{print \$1}')
     reference_transcripts=\$(awk 'NR == 2 {print \$2}' detected_transcripts_genes_numbers.tsv)
-    novel_transcripts=\$(awk 'NR == 2 {print \$2 + \$7}' detected_transcripts_genes_numbers.tsv)
+    novel_transcripts=\$(wc -l string/novel_trid_nbex.txt | awk '{print \$1}')
 
     perl -pe 's/^"([^"]+)".+\$/\$1/g' \\
       ref_expr/ref.annot.tpm0.1.2samples.exons_complete_gnid_nbtr.txt \\