Hi I am getting the following error ;

ERROR! There is a non fastq file in the provided fastq directory: sample_R1.fastq.gz Exiting.

This seems to be coming from cashier.py

for f in fastqs: ext = os.path.splitext(f)[-1].lower() if ext != '.fastq': print('ERROR! There is a non fastq file in the provided fastq directory: {}'.format(f)) print('Exiting.')

Please recommend the file formatting/naming

┤ cashing in...[E::hts_open_format] Failed to open file "/data/sams/possorted_genome_unmapped.sam" : No such file or directory
Traceback (most recent call last):
  File "/opt/conda/bin/pycashier", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.10/site-packages/pycashier/cli.py", line 149, in main
    cli(prog_name="pycashier")
  File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/pycashier/cli.py", line 132, in scrna
    pycashier.scrna(**kwargs)
  File "/opt/conda/lib/python3.10/site-packages/pycashier/pycashier.py", line 163, in scrna
    single_cell(
  File "/opt/conda/lib/python3.10/site-packages/pycashier/single_cell.py", line 231, in single_cell
    single_cell_process(
  File "/opt/conda/lib/python3.10/site-packages/pycashier/single_cell.py", line 147, in single_cell_process
    sam_to_name_labeled_fastq(sample, samfile, fastq, status)
  File "/opt/conda/lib/python3.10/site-packages/pycashier/single_cell.py", line 35, in sam_to_name_labeled_fastq
    with pysam.AlignmentFile(
  File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/sams/possorted_genome_unmapped.sam`: No such file or directory

I've confirmed the file is present and the volume mounted properly.

File searching before extraction/merging attempts to prevent the user from using an unexpected data source.

But it's probably a reasonable assumption there data would not include "hidden" files or anything prepended with a "."

For instance something like .DS_store or .snakemake_timestamp, harmless files that we can ignore without frustrating the user.

pycashier extract doesn't detect if there are paired-end reads...should warn user that they should probably use pycashier merge first.

Also should attempt to detect duplicate files based on sample name extraction.

Additionally, since the first step is quality filtering with fastp it should be possible to supply .fastq.gz without any additional work besides disabling the exclusive .fastq check.