From bdd4cdf94b7dfc36220054e8f7e3a737c558cfb8 Mon Sep 17 00:00:00 2001
From: Carine <carine.rey@ens-lyon.fr>
Date: Fri, 4 Mar 2022 17:51:32 +0100
Subject: [PATCH] fix bug (index bam between star and htseq)
---
src/RNAseq_cec.nf | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_cec.nf b/src/RNAseq_cec.nf
index 37f8cad..2f19bcd 100644
--- a/src/RNAseq_cec.nf
+++ b/src/RNAseq_cec.nf
@@ -26,6 +26,11 @@ include {
star_mapping_fastq_out: "star_bam/"
)
+include { index_bam
+ } from './nf_modules/samtools/main.nf' addParams(
+ htseq_out: "star_bam/"
+)
+
include { htseq_count_with_gff
} from './nf_modules/htseq/main.nf' addParams(
htseq_out: "htseq_count/"
@@ -86,9 +91,12 @@ workflow {
star_index.collect(),
fastp.out.fastq,
)
+
+ //// index bam
+ index_bam(star_mapping_fastq.out.bam)
htseq_count_with_gff(
- star_mapping_fastq.out.bam,
+ index_bam.out.bam_idx,
genome_gff3_file
)
--
GitLab