MicroSALT cannot start single sample case

[beatrizsavinhas]

Describe the bug MicroSALT crashes when running single sample cases with the following errors:

2024-02-15 02:13:31 hasta.scilifelab.se cg.utils.commands[188134] CRITICAL Call ['/home/proj/production/bin/miniconda3/bin/conda run --name P_microSALT', '/home/proj/production/bin/miniconda3/envs/P_microSALT/bin/microSALT', 'analyse', '/home/proj/production/microbial/queries/CASEID.json', '--input', '/home/proj/production/microbial/fastq/CASEID'] exit with a non zero exit code
2024-02-15 02:13:31 hasta.scilifelab.se cg.utils.commands[188134] CRITICAL INFO - Cached resFinder database identical to remote.
INFO - Re-indexed contents of /home/proj/production/microbial/references/resistances
INFO - Re-indexed contents of /home/proj/production/bin/git/microSALT/unique_references
ERROR - Unable to create job for sample SAMPLEID
Source: No files in directory /home/proj/production/microbial/fastq/CASEID match file_pattern '\w{8,12}_\w{6,10}(?:-\d+)*(?:\w+)*_L\d{1,3}_(?:R)*(\d{1})(?:_\d{1,3})*.fastq.gz'.
ERROR - Unable to analyze single sample SAMPLEID
...
FileNotFoundError: [Errno 2] No such file or directory: '/home/proj/production/microbial/results//SAMPLEID_RUN_TIMESTAMP/sampleinfo.json'

To Reproduce Steps to reproduce the behavior:

1. Run workflow-microsalt-start-available or workflow-microsalt-start CASEID on a case with a single sample
2. See error

Expected behavior The case should start with no issues.

Software version (please complete the following information):

• microSALT ?

Additional context