v4.2.3

What's Changed

• Allowing relative paths for submission config by @RamiyapriyaS in #269

Full Changelog: v4.2.2...v4.2.3

v4.2.2

What's Changed

• Update README.md by @RamiyapriyaS in #261
• For verbose (v) and short (s) flags, set valid MM DD dates by @jessicarowell in #264
• Removed old unused general_utility.py script by @RamiyapriyaS in #266

Full Changelog: v4.2.1...v4.2.2

v4.2.1

What's Changed

• Schema and config parameter updates + removed enable_conda parameter by @RamiyapriyaS in #260

Full Changelog: v4.2.0...v4.2.1

v4.2.0

What's Changed

• Added --fetch_reports_only which looks on the NCBI server for report.xml files for the samples in the metadata file the user has indicated, for the databases the user has indicated.
• Redefined --update_submission so it should be used for updating records on BioSample or SRA. It requires valid accession IDs in the submission_report.csv.
• So TOSTADAS now has 3 different submission workflows: --submission runs an initial submission to BioSample, SRA, or Genbank. --fetch_reports_only will look for the report.xml files, and --update_submission should be used to update existing records with valid accession IDs.
• Rework update submissions to allow re-submissions by @jessicarowell in #256

Full Changelog: v4.1.4...v4.2.0

v4.1.4

What's Changed

• Patch to fully integrate the keep_demographic_info and date_format flags by @jessicarowell in #249

Full Changelog: v4.1.3...v4.1.4

v4.1.3

What's Changed

• Patch to allow relative file paths by @RamiyapriyaS in #257

Full Changelog: v4.1.2...v4.1.3

v4.1.2

Changes from Previous Release (v4.1.1):

• Patch to allow for "dots" in sample names in the metadata Excel file

Full Changelog: v4.1.1...v4.1.2

v4.1.1

Changes from Previous Release (v4.1.0):

• Removed legacy code in the VALIDATE_PARAMS process and moved validation plugin to main workflow
• Updated the nextflow_schema.json file to search for file patterns in input parameters
• Updated README to indicate nf-schema warning message in Nextflow version 24 or later.

Full Changelog: v4.1.0...v4.1.1

v4.1.0

Changes from Previous Release (v4.0.0):

(1) New Nextflow validation schema

• Added support for nf-schema@2.1.1 to validate Nextflow parameters in config files
• This plug-in does not work by default on Nextflow version 24.10.0. It will need to be installed first, and this will be tested and added to the README in a future minor update.

(2) Added basic support for custom metadata and BioSample packages

• Users can add custom fields to their metadata file and the custom_fields json template to have those fields added as Attributes in the BioSample submission.xml file
• Users can specify a BioSample package in the submission config file

(4) Environment changes and upgrades

• Fixes a conda envionment issue

(3) Bug fixes

• Patch to required fields in metadata validation (to allow valid strings)
• Fixed a broken while loop
• Allow submission to run without fasta file (updated in both submission modules)
• Patch that fixed several bugs in metadata validation and submission

New Contributors

• @Alan-Collins made their first contribution in #240

Full Changelog: v4.0.0...v4.1.0

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...