From 52e095057db6354e6f040a57aeb4c65d505cf388 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 09:16:26 +0200
Subject: [PATCH] RSEM: change toList to collect
---
src/nf_modules/RSEM/rsem.nf | 4 ++--
src/nf_modules/RSEM/tests/quantification_paired.nf | 2 +-
src/nf_modules/RSEM/tests/quantification_single.nf | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/RSEM/rsem.nf b/src/nf_modules/RSEM/rsem.nf
index 54e6ad0..9a14cc8 100644
--- a/src/nf_modules/RSEM/rsem.nf
+++ b/src/nf_modules/RSEM/rsem.nf
@@ -71,7 +71,7 @@ process mapping_fastq {
input:
set pair_id, file(reads) from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into counts_files
@@ -120,7 +120,7 @@ process mapping_fastq {
input:
file reads from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into count_files
diff --git a/src/nf_modules/RSEM/tests/quantification_paired.nf b/src/nf_modules/RSEM/tests/quantification_paired.nf
index 75ae42f..0109500 100644
--- a/src/nf_modules/RSEM/tests/quantification_paired.nf
+++ b/src/nf_modules/RSEM/tests/quantification_paired.nf
@@ -20,7 +20,7 @@ process mapping_fastq {
input:
set pair_id, file(reads) from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into counts_files
diff --git a/src/nf_modules/RSEM/tests/quantification_single.nf b/src/nf_modules/RSEM/tests/quantification_single.nf
index 0fd26f0..63b2a40 100644
--- a/src/nf_modules/RSEM/tests/quantification_single.nf
+++ b/src/nf_modules/RSEM/tests/quantification_single.nf
@@ -1,6 +1,6 @@
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
-params.mean = 300
+params.mean = 125
params.sd = 100
log.info "fastq files : ${params.fastq}"
@@ -24,7 +24,7 @@ process mapping_fastq {
input:
file reads from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into count_files
--
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