From ef62cf28256ccf811c07888f98ba12690333b8b6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 5 May 2021 08:45:47 +0200
Subject: [PATCH] kb: remove collect() call
---
src/nf_modules/kb/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 0dcc470d..d174b19c 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -101,13 +101,13 @@ workflow count {
.set{ whitelist_optional }
switch(params.kb_protocol) {
case "marsseq":
- split(fastq, config.collect())
- kb_marseq(index.collect(), split.out.fastq.view(), transcript_to_gene, whitelist_optional)
+ split(fastq, config)
+ kb_marseq(index, split.out.fastq.view(), transcript_to_gene, whitelist_optional)
kb_marseq.out.counts.set{res_counts}
kb_marseq.out.report.set{res_report}
break;
default:
- kb_default(index.collect(), fastq, transcript_to_gene, whitelist_optional)
+ kb_default(index, fastq, transcript_to_gene, whitelist_optional)
kb_default.out.counts.set{res_counts}
kb_default.out.report.set{res_report}
break;
@@ -194,7 +194,7 @@ process kb_marseq {
}
def whitelist_param = ""
if (whitelist_id != "NO WHITELIST"){
- whitelist_param = "-w ${white_list}"
+ whitelist_param = "-w ${whitelist}"
}
if (reads.size() == 2)
--
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