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@jessicarowell jessicarowell released this 26 Aug 17:03
v7.0.0
4b07df3
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What's Changed

  • Pipeline split into two separate workflows: biosample_and_sra.nf and genbank.nf. This was necessary because genbank requires assigned biosample accession IDs.

  • Added fasta validation for the Genbank workflow

  • Added a check to exit gracefully if metadata validation log contains ERRORs (i.e., would fail NCBI submission)

  • Added and corrected routing for several log files (mostly in submission subworkflow)

  • Added a new subworkflow to handle fetching reports and aggregating the data

  • Added a process to produce an updated metadata Excel file, with validated contents and accession IDs for BioSample and SRA, if assigned

  • Re-wrote and simplified the wait process (that waits between submitting and fetching reports)

  • Applied many fixes to the source files for the GenBank sqn file (source.src, comment.cmt, authorset.sbt) which were not pulling the correct metadata

  • Refactored to support wastewater data which has a completely different submission.xml file. Use this by setting wastewater flag in nextflow.config to true and by using the wastewater metadata template (ssets/sample_metadata/wastewater_biosample_template.xlsx) and the custom fields file (--custom_fields_file assets/custom_meta_fields/ww_biosample_pkg.json)

  • Many bug fixes

Full Changelog: v6.0.1...v7.0.0

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