0.5.0

The pipeline has been reorganized to, by default, predict each input samples genotype and run with that predicted genotypes set reference and bed file (if running with --amplicon). The functionality to specify a whole run reference and specific primer bed file is kept with the --reference and --primer_bed parameters, which have been made optional.

There are currently 3 supported genotypes (D8, B3, A) and a default fallback reference that users can adjust with either a params-file or on the command line. All genotypes should be supported in the next update. Users are recommended to review these and adjust them based on their internal references and primer files!

Added

• PREDICT_GENOTYPE is a python script that uses minimap2, samtools, and the WHO's N450 measles database to predict the most likely genotype of each sample and automatically selects the appropriate reference for downstream mapping PR #24

• EXTRACT_GENOTYPE is a quick script that retries each reference's genotype and adds it the the reference's meta map for later downstream processes PR #24

• New paramter for read filtering for ONT data PR #24

  • --ont_min_read_length

Adjusted

• Major changes to the pipeline's workflow to create a channel for every process input that requires matching sample and reference data to ensure each process uses the correct reference files that match the sample's genotypePR #24

• Various minor tweaks have been made to input/output handling within processes across the pipeline to support the per-sample worklfow PR #24

• The report generation process was adjusted to allow for a higher memory threshold to allow more samples to be included within one run PR #24

• Tests have been updated and expanded to support the more complicated channel structure and better assess future updates PR #24

  • CI workflow file reformat done to separate out the full workflow test done with the test profiles to be under the ci_workflow.yml file PR #25
    • This is to prevent running the nf-test tests twice as much as necessary

What's Changed

• Addition of prediction script by @AhmedAbdalla4 in #24
• PR for Release of 0.5.0 by @DarianHole in #25

Full Changelog: 0.4.3...0.5.0