From c46cb3887f31a9ab2e9ff53ba865582f01543bd9 Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Fri, 5 Aug 2022 11:11:37 +0200
Subject: [PATCH] Modif Channel idx_genome.
---
src/RNAseq_XGR.nf | 8 ++++----
src/nf_modules/star/main_2.7.8a.nf | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 63cb663..0567db4 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -160,11 +160,11 @@ workflow {
// ref_13 = Channel.fromPath(params.idx +'/transcriptInfo.tab')
// ref_14 = Channel.fromPath(params.idx +'/sjdbList.fromGTF.out.tab')
// ref_15 = Channel.fromPath(params.idx +'/sjdbList.out.tab')
-
// genome_indexed_input = ref_1.concat(ref_2,ref_3,ref_4,ref_5,ref_6,ref_7,ref_8,ref_9,ref_10,ref_11,ref_12,ref_13,ref_14,ref_15)
- // Channel
- // .of( idx_genome )
- // .set { genome_indexed_input }
+
+ Channel
+ .fromPath( "${params.idx}/*" )
+ .set { genome_indexed_input }
mapping_withindex(idx_genome, fastp.out.fastq)
stats_bam(mapping_withindex.out.bam)
filter_bam_mapped(mapping_withindex.out.bam)
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index 91a74dc..ac4a4fd 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -193,7 +193,7 @@ process mapping_withindex {
}
input:
- val(index)
+ path(index)
tuple val(reads_id), path(reads)
output:
--
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