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Bishop-Laboratory / RLPipes

RLPipes: A standardized R-loop-mapping pipeline.
https://anaconda.org/bioconda/rlpipes
MIT License
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Gzipped fastq files do not work #76

Closed millerh1 closed 2 years ago

millerh1 commented 2 years ago

Gzipped fastq files produce the following error:

Traceback (most recent call last):
  File "/home/millerh1/miniconda3/envs/rlpipes/bin/RLPipes", line 10, in <module>
    sys.exit(cli())
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 1137, in __call__
    return self.main(*args, **kwargs)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 1062, in main
    rv = self.invoke(ctx)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 1666, in invoke
    sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 923, in make_context
    self.parse_args(ctx, args)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 1379, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 2364, in handle_parse_result
    value = self.process_value(ctx, value)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/click/core.py", line 2326, in process_value
    value = self.callback(ctx, self, value)
  File "/home/millerh1/miniconda3/envs/rlpipes/lib/python3.9/site-packages/rlpipes/cli.py", line 267, in validate_samples
    samptype = [key for key, val in redict.items() if re.match(val, exp)][0]
IndexError: list index out of range

The problem is the REGEX used for finding FQ files: https://github.com/Bishop-Laboratory/RLPipes/blob/main/rlpipes/cli.py#L57