combine_reports error due to file name truncation

[vasquini]

The samples are truncated at the first "_". So there needs to be some documentation for naming conventions.
executor > local (384)
[c1/7f7539] process > cutadapt (SUS3-M347-23-036) [100%] 48 of 48 ✔
[f7/77b399] process > concat_reads (SUS3-M347-23-036) [100%] 48 of 48 ✔
[8c/59cae4] process > pair_merging (OXA3-M347-23-036) [100%] 48 of 48 ✔
[60/421769] process > quality_filtering (TwistControl-M347-23-036) [100%] 48 of 48 ✔
[03/a016b4] process > dereplication (TwistControl-M347-23-036) [100%] 48 of 48 ✔
[ec/4bca18] process > denoising (TwistControl-M347-23-036) [100%] 48 of 48 ✔
[e6/256cef] process > search_exact (TwistControl-M347-23-036) [100%] 48 of 48 ✔
[fd/3dda6d] process > make_count_table (TwistControl-M347-23-036) [100%] 48 of 48 ✔
[- ] process > combine_reports -
Error executing process > 'combine_reports (combine reports)'

Caused by:
Process combine_reports input file name collision -- There are multiple input files for each of the following file names: AR0043A-M347-23-036.csv

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

I looked into the files passed into the process, and there were indeed doubles.
There's two files with a nearly identical sample name that was not accounted for in the splitting and such:

(hmas3) bash-4.2$ ls -lth /scicomp/instruments/23-7-440_Illumina-MiSeq-M00347/M347-23-036/231019_M00347_0107_000000000-L32J3/Alignment_1/20231021_070701/Fastq/AR0043A-M347-23-036_SR1
-rwxrwxr-x 1 insuser-m00347 users-pure 74M Oct 21 07:15 /scicomp/instruments/23-7-440_Illumina-MiSeq-M00347/M347-23-036/231019_M00347_0107_000000000-L32J3/Alignment_1/20231021_070701/Fastq/AR0043A-M347-23-036_S33_L001_R1_001.fastq.gz
-rwxrwxr-x 1 insuser-m00347 users-pure 31M Oct 21 07:15 /scicomp/instruments/23-7-440_Illumina-MiSeq-M00347/M347-23-036/231019_M00347_0107_000000000-L32J3/Alignment_1/20231021_070701/Fastq/AR0043A-M347-23-036_S2_L001_R1_001.fastq.gz