From 63e1a63cbec22963531a1ddee230ae455b076229 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 1 Feb 2019 14:15:26 +0100
Subject: [PATCH] Addition of output files in finish rule of process_data
Snakefile
---
snakemake/process_data/Snakefile | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/snakemake/process_data/Snakefile b/snakemake/process_data/Snakefile
index bfc0f0c..7df1d42 100644
--- a/snakemake/process_data/Snakefile
+++ b/snakemake/process_data/Snakefile
@@ -1,7 +1,7 @@
configfile: "config.yaml"
#from snakemake.utils import listfiles
-localrules: finish, count_oligos
+localrules: finish
################################################################################
### Finish rule
@@ -9,13 +9,11 @@ localrules: finish, count_oligos
rule finish:
input:
- oligos_counts = expand(os.path.join(config["output_dir"], "{sample}", "oligos_counts.txt"), sample=config["sample"])
-
-
- #pdf = expand(os.path.join(config["output_dir"], "{sample}/read_length/read_length_histogram.pdf"), sample=config["sample"]),
- #counts = expand(os.path.join(config["output_dir"], "{sample}/counts.tsv"), sample=config["sample"]),
- #bai = expand(os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.a_site_profile.sorted.bam.bai"), sample=config["sample"]),
- #overrepresented_sequences_counts = expand(os.path.join(config["output_dir"], "{sample}/overepressented_sequences_other.txt"), sample=config["sample"])
+ oligos_counts = expand(os.path.join(config["output_dir"], "{sample}", "oligos_counts.txt"), sample=config["sample"]),
+ pdf = expand(os.path.join(config["output_dir"], "{sample}/read_length/read_length_histogram.pdf"), sample=config["sample"]),
+ counts = expand(os.path.join(config["output_dir"], "{sample}/counts.tsv"), sample=config["sample"]),
+ bai = expand(os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.a_site_profile.sorted.bam.bai"), sample=config["sample"]),
+ overrepresented_sequences_counts = expand(os.path.join(config["output_dir"], "{sample}/overepressented_sequences_other.txt"), sample=config["sample"])
################################################################################
### Count oligos
--
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