From 0ee9fa4208b984c3e6ad419b53a04f7243b002a6 Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Mon, 25 Jul 2022 13:33:41 +0200
Subject: [PATCH] add STAR and HTseq to RNAseq_XGR.nf
---
src/RNAseq_XGR.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index f456e70..bd67d8b 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -116,7 +116,7 @@ workflow {
//########################## PREPROCESSING ####################
// fastp
- fastp(fastq_files)
+ fastp(fastq_files.collect())
//########################## QUALITY CHECKS ###################
@@ -142,7 +142,7 @@ workflow {
.set { genome_file }
index_with_gtf(genome_file, gtf_file.collect())
- mapping_fastq(index_with_gtf.out.index, fastq_files)
+ mapping_fastq(index_with_gtf.out.index, fastp.out.fastq)
}
else {
idx_genome = "${params.idx}/*"
@@ -150,7 +150,7 @@ workflow {
.fromPath( idx_genome )
.ifEmpty { error "Cannot find idexed genome reference files" }
.set { genome_indexed_input }
- mapping_fastq(genome_indexed_input, fastq_files)
+ mapping_fastq(genome_indexed_input, fastp.out.fastq)
}
//######################## HTseq COUNT #########################
--
GitLab