[Internal] [Bug] New code not generating report.xml after submission

[jessicarowell]

Files are getting submitted to test server, but report.xml not being generated.

Place an :x: in a Box that Best Matches the Bug's Importance:

• [x] 1 - Most severe (a full-break in core function)
• [] 2-4 - Moderate (break for a particular aspect/feature) (how integral is the broken feature?)
• [] 5 - Least severe (non-functional issue, such as inconsitency / error in documentation or administrative in nature) 

Please Complete the Following Information:

• OS: [e.g. iOS]:
• Browser [e.g. chrome, safari]:
• Version [e.g. 22]:
• Run environment (container, cloud service, HPC, platform, etc.):

nextflow run main.nf -profile test,singularity --species mpxv --submission --annotation --genbank true --sra true --submission_wait_time 2 --output_dir test3 --meta_path /scicomp/home-pure/ick4/01.scripts/tostadas/assets/sample_metadata/mpxv_user_provided_annotations_metadata.x lsx --submission_config /scicomp/home-pure/ick4/02.scratch/submission_config.yaml -resume