From a368aae1d8e8beb6954282bba1d0484323cb4279 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Fri, 7 Jun 2019 10:05:59 +0200
Subject: [PATCH] 1000RNASeq_chicken ASE : change rule names
---
Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
index 8df1b00..685105b 100644
--- a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
+++ b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
@@ -12,7 +12,7 @@ wildcard_constraints:
STAR_INDEX_FILE=['genomeParameters.txt', 'chrName.txt', 'chrLength.txt', 'chrStart.txt', 'chrNameLength.txt', 'exonGeTrInfo.tab', 'geneInfo.tab', 'transcriptInfo.tab', 'exonInfo.tab', 'sjdbList.fromGTF.out.tab', 'sjdbInfo.txt', 'sjdbList.out.tab', 'Genome', 'SA', 'SAindex']
-rule STAR_Index:
+rule STAR_Index_1:
input:
fasta = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.fa',
gtf = os.path.abspath(config["gtf_ref"])
@@ -157,7 +157,7 @@ def get_properly_paired_bam(wildcards):
return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic.bam"
-rule rmdup:
+rule RmDuplicates:
input:
bam = get_properly_paired_bam
output:
--
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