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#657 Validate input files from config file #821

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#657 Validate input files from config file #821

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19ecc1e
Attempted to fix issue 700 by for including metadata on line 503
emontag47 Dec 14, 2021
555fd09
Attempted to fix issue 463 by checking subsampling scheme against lis…
emontag47 Dec 14, 2021
a50ad58
Attempted to fix issue 657 by adding new function that checks input f…
emontag47 Dec 14, 2021
fb67fa7
move issue fix to other branch
emontag47 Dec 14, 2021
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8 changes: 8 additions & 0 deletions workflow/snakemake_rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -168,3 +168,11 @@ def _get_upload_inputs(wildcards):
else:
raise Exception("The upload rule requires an 'upload' parameter in the config.")

def _check_input_files(wildcards):
# function that checks the config["inputs"] and check local files to make sure input file exists

for file in config["inputs"]:
if ' ' in file:
raise Exception("The inputted file {} has an invalid name as it contains spaces. Please remove them and try again.".format(file))
if not os.path.exists(file):
raise Exception("The inputted file {} does not exist. Please input a valid file and try again.".format(file))