changes to the paths of custom scripts in local modules for cloud computing

[cjjossart]

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When running the CDCgov/mycosnp-nf v 1.4 pipeline in the cloud (AWS-Batch through Nextflow-tower) an error is raised due to not being able to find the custom scripts used in local modules (i.e. no such file or directory).
I believe this is happening, because $projectDir is used as part of the file path for these scripts. Locally this would be fine.

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A potential solution for this issue could be:

1. Move all custom scripts to the bin folder, if not there already
   - move scripts and contents of broad-vcf-filter folder up one directory into the bin folder.
2. Execute scripts by name (i.e. qc_report_stats.py) in local modules instead of using python command and path to script (i.e. $projectDir/bin/qc_report_stats.py).
3. Update any instances of changed file paths for custom scripts.

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This possible solution works locally and in the cloud with aws-batch.
I can submit a PR with these changes if this makes sense.
Please reach out if there is a better solution to this issue and if there is a reason for the current way the custom scripts are called in local modules.

Thanks and sincerely,

CJ