Update to version 0.4.0 #106
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fixed typos
* starting locidex database integrations * updated added new files * updated locidex db identification * updated automated allele selection * updated todos * added test data for locidex databases, tests should still function: * updated nextflow schema.json * Removed tests for comparing updates for old and new locidex profiles Perhaps the relevant fields should be sub set out * removed dead test file * updated test profile * restrucutured file staging for locidex select * started creation of real tests for locidex workflow * updated locidex test data * updated locidex workflow and tests * updated docker container * addressed PR issues, still more work to be done * updated database selection functions to get an optimal match * added skipped allele calling to test config * updated test conditions * updated test files * updated locidex select paths * removed trailing whitespace * updated tests to include passing cases * added locidex summary process * updated fixe issues with integer sizing * debugging summary test * Added field for reportable alleles * updated reportable loci test * updated locidex summary tests * updated missing allelels JSON type * upated not database selected output * updated IRIDANEXT config for locidex values * updated locidex end-to-end tests * updated locations of locidex test * zipped and updated sample datasets * upated locidex end to end tests * fixed typos in change log * updated locidex tests * cleaned up datebase name parsing * fixed code comment * updated code comments * made updates on PR comments * normalized output for iridanext across allele scheme input options * updated test cases * updated locidex_select tests to match updated interface * updated test to work in github actions * removed sneaky todo * updating issues identified and regression in kraken2 header parsing * reverted zipped file handling * fixed regression locidex select * removed repeated variables * updated staging of report input to locidex summarize * updated file parsing in locidex summarize Thank you Aaron! * updated changelog * extracted inline code in function * bumped locidex container * updated final todos * updated options to locidex_select test to terminate processes on failure
…LST (#98) * updated Torsteins mlst container, as results were differing with PubMLST * updated wordslist * updated test to use e.coli achtman 4 * update listeria scheme selection * updated changelog statement
#102) * updated tests running average coverage calculations in cloud executors * committing progress, difference in behaviour between nextflow versions is being observed * fixed missing coverage value in version 24 of nextflow * updated test ouputs * removed docker.userEmulation as marked as deprecated * renamed duplicated test name
…ault container option
dropped quay.io from docker paths
* fixed typo and metagenomic QCSummary message * updated changelog * removed comma * updated metagenomic tests * added missing test files * updated virus mash sketch * updated output values * fixed test typo * reintegrated deleted test
* updated config defaults for various organisms * updated changelog
* updated parameters for allele schema * updated changelog * fixed error in parameter updates * fixed misspelled param * updated test config * updated CLI argument * dropped allele scheme used from the irida-next config * updated tests to pass * updated container default settings * updated changelog and version
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Update mikrokondo to version 0.4.0.
See
CHANGELOG.mdfor updates.