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SAMPLESHEET_CHECK fails on sample sheet with many sample lines #1561

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praveenraj2018 opened this issue May 11, 2022 · 0 comments · Fixed by #1584
Closed

SAMPLESHEET_CHECK fails on sample sheet with many sample lines #1561

praveenraj2018 opened this issue May 11, 2022 · 0 comments · Fixed by #1584
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@praveenraj2018
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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 here

samplesheet_large.csv

Command used and terminal output

$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_VERSIONS

Command exit status:
  1

Command 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

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