Release 4.0.0

Changes from Previous Release (v3.1.0):

(1) New, streamlined submission code

• Supports ftp submission to GenBank (SARS-CoV-2, influenza, and bacteria)
• GenBank ftp submission uses table2asn (v1.28.1179) to prepare an ASN.1 file, authorset.sbt file, and comment.cmt file and uploads these to NCBI along with a submission.xml file.
• Still support non-ftp GenBank submission, either manually (send the email yourself) or automatically send submission to user and NCBI GenBank submission team. This mode uses table2asn to prepare an ASN.1 file, authorset.sbt, comment.cmt, and source.src file. IT also creates a zip file of these extra table2asn outputs.
• Change name of raw fastq files to <sample_name>_R{1,2}.fastq.gz (important: code assumes your fastq files are gzipped) before ftp upload to SRA repository.
• Added support for SRA publication hold (delayed release)
• Note: Submissions are currently completed one sample at a time. Batch submissions coming soon.
• SFTP support added (still in beta testing)

(2) Minor corrections to metadata files

• Two columns adjusted to clarify input and to match NCBI attribute name (age and sex --> host_age and host_sex)
• Extraneous "description" column removed from metadata files
• gff_path added to some test metadata files where it was missing
• "Cdiphtheriae" changed to "bacteria" in test data, for added clarity

(4) Environment changes and upgrades

• table2asn added to environment.yml file
• nameparser (v1.0.5) python library added to environment.yml file
• paramiko (v3.4.0) python library added to environment.yml file

(3) Bug fixes

• Several bug fixes were made along the way...