Can't process whitespaces in the read filenames

[nromashchenko]

Read2Tree version: 2.0.1

It seems if read files name have whitespaces, they are either not correctly passed to mafft, or mafft itself is unhappy.

To reproduce: proceed with the test example given in the README. Then

cd tests
cp sample_1.fastq "sample_1 copy.fastq"
cp sample_2.fastq "sample_2 copy.fastq"
read2tree --tree --standalone_path marker_genes --reads sample_1\ copy.fastq  sample_2\ copy.fastq --output_path ./output --dna_reference dna_ref.fa

...
d2tree-test/bin/mafft --auto --thread 1 --maxiterate 1000 --amino /tmp/tmp9vel2wo0
2025-11-12 15:22:14 INFO     sample_1 copy: Alignment of 20 OGs took 5.6129608154296875.
--- Mapping of reads to reference sequences ---
Mapping reads to species:   0%|                              | 0/5 [00:00<?, ? species/s]2025-11-12 15:22:14 INFO     sample_1 copy: --- Mapping of reads to MNELE reference species ---
Mapping reads to species:   0%|                              | 0/5 [00:00<?, ? species/s]

after which it stops with an error without providing any information.

> echo $?
1

[sinamajidian]

We expect users not to include whitespace or special characters in file names. But it won't hurt to allow it for sure.

[nromashchenko]

I only need this for the galaxy wrapper which renames filenames wildly under the hood... also adding whitespaces. For now I think I can work around this, but I am afraid, I am not the only one who expects it to work if filename is escaped or in double quotes