From 972e601e3fbaa532ae7b70ead37aac71856a9f61 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 7 May 2021 16:25:18 +0200
Subject: [PATCH] kb: remove view()
---
src/nf_modules/kb/main.nf | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index e5895ba6..32297d25 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -102,7 +102,7 @@ workflow count {
switch(params.kb_protocol) {
case "marsseq":
split(fastq, config)
- kb_marseq(index.collect(), split.out.fastq.view(), transcript_to_gene, whitelist_optional)
+ kb_marseq(index.collect(), split.out.fastq, transcript_to_gene, whitelist_optional)
kb_marseq.out.counts.set{res_counts}
kb_marseq.out.report.set{res_report}
break;
@@ -210,4 +210,17 @@ process kb_marseq {
-o ${file_prefix} \
${reads[0]} ${reads[1]} &> ${file_prefix}_kb_mapping_report.txt
"""
+ else
+ """
+ mkdir ${file_prefix}
+ kb count -t ${task.cpus} \
+ -m ${kb_memory} \
+ -i ${index} \
+ -g ${transcript_to_gene} \
+ ${whitelist_param} \
+ ${params.count} \
+ -x 1,0,6:1,6,14:1,14,0
+ -o ${file_prefix} \
+ ${reads} &> ${file_prefix}_kb_mapping_report.txt
+ """
}
\ No newline at end of file
--
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