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Commit f5e7f5b7 authored by BIOPZ-Bak Maciej's avatar BIOPZ-Bak Maciej
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fixed '/' issue in the code

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1 merge request!56fix absolute / relative path issue in fastqc results parsing
Pipeline #10546 passed
Stage: test
This commit is part of merge request !56. Comments created here will be created in the context of that merge request.
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......@@ -1113,8 +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]))
if params.results_dir.startswith("/"): new_path = "/" + new_path
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(
......
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