[Internal] [Bug] GenBank folder not showing up in outdir/submission_outputs

[jessicarowell]

When running genbank submission, the genbank folder is created, will all the files, but only shows up in the INITIAL_SUBMISSION workdir.

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

• [] 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.):

Steps to replicate

nextflow run main.nf -profile test,singularity --species virus --submission --sra --biosample --genbank --output_dir test --submission_config ~/02.scratch/submission_config.yaml

Example workdir contents ../f7/7befbd11d26f189e1a1d878500848d/NY0006 :
biosample/
genbank/
sra/

Published output for that sample: ls test/submission_outputs/NY0006 :
biosample
sra

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Concrete Instructions to Resolve the Bug or Helpful Resources to Reference? Screenshots or Logs?

Publish directive in modules/initial_submission/main.nf :
publishDir "$params.output_dir/$params.submission_output_dir", mode: 'copy', overwrite: params.overwrite_output

[jessicarowell]

Fixed (commit #2d81db2)