The get_reads() function in common.smk results in spaces being inserted into fastq files in Python 3.12:
File path ' results/data/fastq/ GCF_001447265.1 / SAMN04029017 / SRR2240703 _1.fastq.gz ' starts with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
This probably has to do with changes to how f-strings are parsed in Python 3.12 (see here), but it is not obvious to me exactly how things are going wrong.
The get_reads() function in common.smk results in spaces being inserted into fastq files in Python 3.12:
This probably has to do with changes to how f-strings are parsed in Python 3.12 (see here), but it is not obvious to me exactly how things are going wrong.