From 3716b5ae002ca8dd374fdf93f2817b196d13adc2 Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Tue, 26 Jul 2022 09:59:07 +0200
Subject: [PATCH] Modif RNAseq_XGR.nf to provide indexed STAR genome
---
src/RNAseq_XGR.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 85e26d2..3241542 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -149,12 +149,13 @@ workflow {
}
else {
idx_genome = "${params.idx}"
- Channel
+ /* Channel
.fromPath( idx_genome )
.ifEmpty { error "Cannot find idexed genome reference files" }
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { genome_indexed_input }
- mapping_withindex(genome_indexed_input.collect(), fastp.out.fastq)
+ */
+ mapping_withindex(idx_genome, fastp.out.fastq)
htseq_count(mapping_withindex.out.bam, gtf_file)
}
}
--
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