From ecc71f7d6b93559f0814f26c973bc7d75fb1620e Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 24 Jan 2020 18:29:53 +0100
Subject: [PATCH] Fix params.direcionality for kallisto rule
---
snakemake/paired_end.snakefile | 2 +-
snakemake/single_end.snakefile | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/snakemake/paired_end.snakefile b/snakemake/paired_end.snakefile
index 23fb6e9..3488d27 100644
--- a/snakemake/paired_end.snakefile
+++ b/snakemake/paired_end.snakefile
@@ -335,7 +335,7 @@ rule pe_genome_quantification_kallisto:
-i {input.index} \
-o {params.output_dir} \
--pseudobam \
- --{params.directionality}-stranded \
+ {params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) &> {log}"
diff --git a/snakemake/single_end.snakefile b/snakemake/single_end.snakefile
index 7c6b2ac..5c06dac 100644
--- a/snakemake/single_end.snakefile
+++ b/snakemake/single_end.snakefile
@@ -259,7 +259,7 @@ rule genome_quantification_kallisto:
-l {params.fraglen} \
-s {params.fragsd} \
--pseudobam \
- --{params.directionality}-stranded \
+ {params.directionality} \
{input.reads} > {output.pseudoalignment}) &> {log}"
\ No newline at end of file
--
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