issue of f-string in snakemake and python 3.12 makes extra whitespaces in get_input_fastqs

simonlabcode / bam2bakR

2 stars 0 forks source link

issue of f-string in snakemake and python 3.12 makes extra whitespaces in get_input_fastqs #8

Closed realzhang closed 10 months ago

realzhang commented 1 year ago

Dear authors: In workflow/rules/common.smk, the f-string in glob.glob to match input fastq filenames may introduce one whitespace before and after "fastq_path". refer to: https://github.com/snakemake/snakemake/issues/2480 I've changed the f-string into '+' to concat the strings. Thanks for your great tools!

isaacvock commented 1 year ago

Hello,

Thank you very much for flagging this. Unfortunately there is another Python 3.12 related issues that will likely force bam2bakR users to run Snakemake in an environment with a Python version < 3.12 installed. I have updated the documentation accordingly and will work on a patch to fix these issues. I'll keep this issue opened until that patch is released.

Thank you for your kind words, Isaac

isaacvock commented 10 months ago

The issue has been addressed in version 3.0.0 of bam2bakR (though technically it is no longer a problem for version 8.4.0+ of Snakemake). This update also includes an unrelated significant decrease in bam2bakR's runtime, discussed in the updated README.

Let me know if you have any questions, Isaac