From 3de4d8def338e1406c55b1cb917f0933edc2fbe9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 28 May 2021 16:40:11 +0200
Subject: [PATCH] example_marseq.nf: add illumina adaptor removal
---
src/example_marseq.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/example_marseq.nf b/src/example_marseq.nf
index 8b8068a9..fb3f8e8f 100644
--- a/src/example_marseq.nf
+++ b/src/example_marseq.nf
@@ -4,6 +4,7 @@ nextflow.enable.dsl=2
Testing pipeline for marseq scRNASeq analysis
*/
+include { adaptor_removal} from "./nf_modules/cutadapt/main.nf"
include { index_fasta; count } from "./nf_modules/kb/main.nf" addParams(
kb_protocol: "marsseq",
count_out: "quantification/"
@@ -57,6 +58,7 @@ channel
.set { config_files }
workflow {
+ adaptor_removal(fastq_files)
index_fasta(fasta_files, cdna_files, gtf_files)
- count(index_fasta.out.index, fastq_files, index_fasta.out.t2g, whitelist_files, config_files)
+ count(index_fasta.out.index, adaptor_removal.out.fastq, index_fasta.out.t2g, whitelist_files, config_files)
}
--
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