From b0a1a53c864fd62e8defc88e3f5d90f0d5a5f810 Mon Sep 17 00:00:00 2001
From: Maciej Bak <maciej.bak@unibas.ch>
Date: Fri, 20 Mar 2020 15:42:07 +0100
Subject: [PATCH] renamed plot file 4 proper parsing
---
Snakefile | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 44bf7b5..9876c72 100644
--- a/Snakefile
+++ b/Snakefile
@@ -963,10 +963,10 @@ rule prepare_files_for_report:
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
- alfa_concat_out = expand(os.path.join(
+ alfa_concat_out = os.path.join(
config["output_dir"],
"ALFA",
- "ALFA_plots.concat.png"))
+ "ALFA_plots.concat.png")
output:
samples_dir = directory(os.path.join(
@@ -1165,6 +1165,14 @@ rule prepare_files_for_report:
params.results_dir,
"TIN scores_mqc.pdf"))
+ # adjust alfa plot filename for MutliQC recognition
+ os.rename(
+ input.alfa_concat_out,
+ os.path.join(
+ params.results_dir,
+ "ALFA",
+ "ALFA_plots.concat_mqc.png"))
+
rule prepare_MultiQC_config:
'''
@@ -1223,6 +1231,10 @@ rule prepare_MultiQC_config:
YAML.write(" path_filters:\n")
YAML.write(" - \"*/map_genome/*\"\n")
YAML.write("\n")
+ YAML.write(" - alfa:\n")
+ YAML.write(" path_filters:\n")
+ YAML.write(" - \"*/ALFA_plots.concat_mqc.png\"\n")
+ YAML.write("\n")
YAML.write(" - TIN_scores:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/TIN scores_mqc.png\"\n")
--
GitLab