From 2792d1e61387d6f2d0b20146effbb30fe29e2634 Mon Sep 17 00:00:00 2001
From: BIOPZ-Bak Maciej <maciej.bak@unibas.ch>
Date: Sun, 22 Mar 2020 17:47:56 +0100
Subject: [PATCH] fix absolute / relative path issue in fastqc results parsing
---
Snakefile | 44 ++++++++++++++++++++++++++++----------------
1 file changed, 28 insertions(+), 16 deletions(-)
diff --git a/Snakefile b/Snakefile
index f71135a..4a43003 100644
--- a/Snakefile
+++ b/Snakefile
@@ -970,7 +970,7 @@ rule prepare_files_for_report:
output:
samples_dir = directory(os.path.join(
- "{output_dir}",
+ config["output_dir"],
"samples"))
params:
results_dir = config["output_dir"],
@@ -979,9 +979,12 @@ rule prepare_files_for_report:
config["log_dir"],
"samples")
log:
- LOG_local_log = \
- os.path.join("{output_dir}", "local_log", \
- "prepare_files_for_report.log")
+ stderr = os.path.join(
+ config["log_dir"],
+ "prepare_files_for_report.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "prepare_files_for_report.stdout.log")
run:
# remove "single/paired end" from the results directories
@@ -1110,7 +1113,9 @@ rule prepare_files_for_report:
for zipfile in fastq_zip_list:
sample_name = zipfile.split("/")[-3]
zipfile_path_chunks = zipfile.split("/")
- new_path = os.path.join(*(zipfile_path_chunks[:-1]))
+ new_path = os.path.abspath(
+ os.path.join(
+ *(zipfile_path_chunks[:-1])))
with ZipFile(zipfile, 'r') as zip_f:
zip_f.extractall(new_path)
fastqc_data_f = os.path.join(
@@ -1180,11 +1185,11 @@ rule prepare_MultiQC_config:
'''
input:
multiqc_input_dir = os.path.join(
- "{output_dir}",
+ config["output_dir"],
"samples")
output:
multiqc_config = os.path.join(
- "{output_dir}",
+ config["output_dir"],
"MultiQC_config.yaml")
params:
logo_path = os.path.join(
@@ -1194,9 +1199,12 @@ rule prepare_MultiQC_config:
"logo.128px.png"),
results_dir = config["output_dir"]
log:
- LOG_local_log = \
- os.path.join("{output_dir}", "local_log", \
- "prepare_MultiQC_config.log")
+ stderr = os.path.join(
+ config["log_dir"],
+ "prepare_MultiQC_config.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "prepare_MultiQC_config.stdout.log")
run:
with open(output.multiqc_config, "w") as YAML:
YAML.write("---\n\n")
@@ -1259,15 +1267,19 @@ rule MULTIQC_report:
config["output_dir"],
"MultiQC_config.yaml")
output:
- MultiQC_report = \
- directory(os.path.join("{output_dir}", "multiqc_summary"))
+ MultiQC_report = directory(os.path.join(
+ config["output_dir"],
+ "multiqc_summary"))
params:
results_dir = config["output_dir"],
log_dir = config["log_dir"]
log:
- LOG_local_log = \
- os.path.join("{output_dir}", "local_log", \
- "MULTIQC_report.log")
+ stderr = os.path.join(
+ config["log_dir"],
+ "MULTIQC_report.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "MULTIQC_report.stdout.log")
singularity:
"docker://ewels/multiqc:1.7"
shell:
@@ -1277,5 +1289,5 @@ rule MULTIQC_report:
--config {input.multiqc_config} \
{params.results_dir} \
{params.log_dir} \
- &> {log.LOG_local_log};
+ 1> {log.stdout} 2> {log.stderr}
"""
--
GitLab