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check_samplesheet.py is throwing an error when the sample sheet has many sample lines. Attached is a sample sheet that failed.
This bug has been first reported by a user (m3hdad) while running rnavar pipeline and I have replicated the issue with a test sheet - attached here
$nextflow run nf-core/rnavar -r dev -profile test,docker --input samplesheet_large.csv......<output truncated>......Error executing process > 'NFCORE_RNAVAR:RNAVAR:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_large.csv)'Caused by: Process `NFCORE_RNAVAR:RNAVAR:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_large.csv)` terminated with an error exit status (1)Command executed: check_samplesheet.py \ samplesheet_large.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_RNAVAR:RNAVAR:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONSCommand exit status: 1Command output: (empty)Command error: Traceback (most recent call last): File "/data2/praveen/rnavar_eval/test_data/rnavar/bin/check_samplesheet.py", line 250, in <module> sys.exit(main()) File "/data2/praveen/rnavar_eval/test_data/rnavar/bin/check_samplesheet.py", line 246, in main check_samplesheet(args.file_in, args.file_out) File "/data2/praveen/rnavar_eval/test_data/rnavar/bin/check_samplesheet.py", line 186, in check_samplesheet reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) File "/data2/praveen/rnavar_eval/test_data/rnavar/bin/check_samplesheet.py", line 149, in sniff_format if not sniffer.has_header(peek): File "/usr/local/lib/python3.9/csv.py", line 393, in has_header rdr = reader(StringIO(sample), self.sniff(sample)) File "/usr/local/lib/python3.9/csv.py", line 187, in sniff raise Error("Could not determine delimiter") _csv.Error: Could not determine delimiter
System information
Python 3.8.8
nextflow version: 21.10.6
The text was updated successfully, but these errors were encountered:
Description of the bug
check_samplesheet.py
is throwing an error when the sample sheet has many sample lines. Attached is a sample sheet that failed.This bug has been first reported by a user (m3hdad) while running
rnavar
pipeline and I have replicated the issue with a test sheet - attached heresamplesheet_large.csv
Command used and terminal output
System information
Python 3.8.8
nextflow version: 21.10.6
The text was updated successfully, but these errors were encountered: