Handle spcaes in raw/mzML file names

[ajmaurais]

• Make sure we are able to handle mzML and raw files with spaces or other crazy characters in the file name
• Fix a small bug in workflows/get_mzmls.nf where error messages weren't being printed properly in some cases

[mriffle]

How come you removed the quotes around all the files being created, except for the .dia one? Aren't those quotes necessary to support mzML files with spaces in the name?

[ajmaurais]

Nextflow will automatically escapes spaces when it is expanding file variables but not the methods for file variables. So ${mzml_file} would expand to file\ with_space.mzML , but ${mzml_file.baseName} would expand to file with_space

[ajmaurais]

If we keep the quotes, when it expands "${mzml_file}.elib" it will create a file name with a literal \ character in the file name

[mriffle]

I am curious about this. Why was adding the -d option necessary?

[ajmaurais]

-d'\n' tells xargs to use new lines as the delimiter instead of all white space, which is the default. Each file is on it's own line in all_files.txt so xargs will parse each line as an argument regardless of whether the file name has spaces

[mriffle]

Ah, thought new lines were the default, makes sense, thanks.

[ajmaurais]

So did I until I was getting an error on this step