From d448ef6abbaeef1dc84078a19fd81a3c430e93e2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 28 May 2021 16:34:26 +0200
Subject: [PATCH] kb: working marseq quantif pipeline
---
src/nf_modules/kb/main.nf | 22 ++++------------------
1 file changed, 4 insertions(+), 18 deletions(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 241c7776..4d3d1fe4 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -9,13 +9,9 @@ workflow index_fasta {
fasta
cdna
gtf
- transcript_to_gene
main:
- transcript_to_gene
- .ifEmpty(["NO T2G", ""])
- .set{ transcript_to_gene_optional }
- tr2g(gtf, transcript_to_gene_optional)
+ tr2g(gtf)
index_default(fasta, cdna, gtf, tr2g.out.t2g)
emit:
@@ -35,23 +31,13 @@ process tr2g {
input:
tuple val(file_id), path(gtf)
- tuple val(t2g_id), file(transcript_to_gene)
output:
tuple val(file_id), path("t2g.txt"), emit: t2g
script:
-
- if (t2g_id == "NO T2G")
- """
- t2g.py --gtf ${gtf} && \
- mv t2g.txt t2g_to_fix.txt && \
- sed -E 's/\\.[0-9]+//g' t2g_to_fix.txt | \
- awk '{print(\$1 "\\t" \$2)}' > t2g.txt
- """
- else
"""
- mv ${transcript_to_gene} t2g.txt
+ t2g.py --gtf ${gtf}
"""
}
@@ -210,7 +196,7 @@ process kb_marseq {
-o ${file_prefix} \
${whitelist_param} \
${params.count} \
- -x 1,0,6:1,6,14:1,14,0 \
+ -x 1,0,6:1,6,14:0,0,0 \
${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
"""
else
@@ -223,7 +209,7 @@ process kb_marseq {
-o ${file_prefix} \
${whitelist_param} \
${params.count} \
- -x 1,0,6:1,6,14:1,14,0 \
+ -x 1,0,6:1,6,14:0,0,0 \
${reads} > ${file_prefix}_kb_mapping_report.txt
"""
}
\ No newline at end of file
--
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