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fix absolute / relative path issue in fastqc results parsing

Merged BIOPZ-Bak Maciej requested to merge fastqc_parsing_bugfix into master
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@@ -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")
@@ -1204,7+1212,7 @@
YAML.write("subtitle: \"RNA-Seq processing pipeline developed by the members of Zavolan Lab\"\n")
YAML.write("intro_text: \"Short analysis title from config[analysis_title]\"\n")
YAML.write("custom_logo: \""+params.logo_path+"\"\n")
YAML.write("custom_logo_url: \"https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/\"\n")
YAML.write("custom_logo_title: \"ZavoLab\"\n\n")
YAML.write("report_header_info:\n")
YAML.write(" - Project Type: \"Snakemake workflow\"\n")
@@ -1245,7+1253,7 @@
YAML.write("\n")
YAML.write(" - kallisto:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/genome_quantification_kallisto.stderr.log.MODIFIED\"\n")
YAML.write("\n")
YAML.write("...")
@@ -1259,7+1267,7 @@
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}
"""
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