From 8ddc3ee6a5d10f30f60bd34e475fe437da0e921d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 17:40:34 +0200
Subject: [PATCH] kallisto: fix typo :47
---
src/nf_modules/kallisto/main.nf | 2 +-
src/solution_RNASeq.nf | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 0546d790..2a0c1ed1 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -44,7 +44,7 @@ kallisto quant -i ${index} -t ${task.cpus} \
${params.mapping_fastq} -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
"""
-else:
+else
"""
mkdir ${pair_id}
kallisto quant -i ${index} -t ${task.cpus} --single \
diff --git a/src/solution_RNASeq.nf b/src/solution_RNASeq.nf
index 1f43fd1f..1a844b01 100644
--- a/src/solution_RNASeq.nf
+++ b/src/solution_RNASeq.nf
@@ -21,16 +21,16 @@ Channel
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
-include { adaptor_removal_pairedend } from './nf_modules/cutadapt/main'
-include { trimming_pairedend } from './nf_modules/urqt/main'
+include { adaptor_removal } from './nf_modules/cutadapt/main'
+include { trimming } from './nf_modules/urqt/main'
include { fasta_from_bed } from './nf_modules/bedtools/main'
-include { index_fasta; mapping_fastq_pairedend } from './nf_modules/kallisto/main'
+include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main'
workflow {
- adaptor_removal_pairedend(fastq_files)
- trimming_pairedend(adaptor_removal_pairedend.out.fastq)
+ adaptor_removal(fastq_files)
+ trimming(adaptor_removal_pairedend.out.fastq)
fasta_from_bed(fasta_files, bed_files)
index_fasta(fasta_from_bed.out.fasta)
- mapping_fastq_pairedend(index_fasta.out.index.collect(), trimming_pairedend.out.fastq)
+ mapping_fastq(index_fasta.out.index.collect(), trimming_pairedend.out.fastq)
}
--
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