Release v1.4.1 · theiagen/terra_utilities

This patch release implements improvements to the Terra_2_NCBI workflow.

Terra_2_NCBI has been modified in the following ways:

single-end reads are now supported
different read1/read2 files can now be indicated using new optional variables read1_column_name and read2_column_name (default columns used: "read1" and "read2")
samples that are excluded due to missing required metadata now tell you what data they are missing
a bug fix was implemented that prevents failure in the rare case where the original sample id consisted of only numbers
several variables are now renamed to be more clear and intuitive:
- biosample_type is now biosample_package
- gcp_bucket_uri is now sra_transfer_gcp_bucket
- MAJOR CHANGE: path_on_ftp_server is now a Boolean variable called submit_to_production where it is by default false, meaning that a Test submission will be performed. If set to true, then a Production submission will occur.

In rare cases, SRA_Fetch would unintentionally overwrite the forward read file (*_R1 file) with singleton reads. This will no longer happen.
For the Concatenate_Column_Content and Zip_Column_Content workflows, call caching is now always off, even if the box is checked.

Improvements to Terra_2_NCBI by @sage-wright in #33
Check to avoid capture of singletons as forward reads by @kevinlibuit in #31
call caching always off for concatenate_column_content and zip_column_content wfs & update terra_2_bq workflow by @kapsakcj in #29
update version by @sage-wright in #34

Full Changelog: v1.4.0...v1.4.1