From 734051f9809cee7a99a7b132c5283ac471de17a2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 19 Aug 2021 10:02:46 +0200
Subject: [PATCH] kb: add g2t process
---
src/nf_modules/kb/main.nf | 24 +++++++++++++++++++++++-
1 file changed, 23 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index d27e84fb..ca4e7552 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -38,7 +38,29 @@ process tr2g {
"""
t2g.py --gtf ${gtf}
sort -k1 -u t2g_dup.txt > t2g.txt
- cp t2g.txt t2g.txt.back
+ """
+}
+
+process g2tr {
+ // create gene to transcript table from gtf if no transcript to gene file is provided
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+ if (params.index_fasta_out != "") {
+ publishDir "results/${params.index_fasta_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(gtf)
+
+ output:
+ tuple val(file_id), path("g2t.txt"), emit: g2t
+
+ script:
+ """
+ t2g.py --gtf ${gtf}
+ sort -k1 -u t2g_dup.txt > t2g.txt
+ awk 'BEGIN{OFS="\\t"}{print \$2, \$1}' t2g.txt > g2t.txt
"""
}
--
GitLab