Misuse of rstrip in make_variants_long_table.py script

[fmaguire]

Hi folks.

There is a problem with the use of rstrip to remove file suffixes at https://github.com/nf-core/viralrecon/blob/master/bin/make_variants_long_table.py#L47 that can cause issues (and a workflow failure) for some sample names.

rstrip doesn't remove a specified substring from the end of string.
It actually removes any characters (and any number of them) regardless of order in the substring from the end of string.
rstrip only stops when it encounters a character in the string not in the specified substring.
e.g.,

"abaaacccca....ccaac".rstrip("ac.")
>>> "ab"

This means sample names containing characters in the suffix being removed get mangled:

filename='XXXX_P0_meta.oilcans.saponin.pangolin.csv'
suffix=".pangolin.csv"
print(filename.rstrip(suffix))
>>>XXXX_P0_met

Replacing rstrip with removesuffix should fix this in python >=3.9 (alternatively replace should be fine although a simple regex would be better!).

[drpatelh]

Hi @fmaguire ! Thanks for reporting! Created a patch release for v2.3.1 that I will get out today. A single word change turned into a bit of a 🐰 🕳️ and I have updated a bunch of other stuff too.

[fmaguire]

Hah, cheers!

I figured it might (e.g., which python version is used etc) despite being a seeming trivial fix, that is why I didn't just submit a quick PR.

[drpatelh]

Release done 🎉 https://github.com/nf-core/viralrecon/releases/tag/2.3.1