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Improve the way the layout column is checked and remove the test parameter and functionality in load_config as it has become clear that implementing unit tests will require its own issues and resolutions
Make sure the table is in fact an SRA sampletable before checking the layout
add function creating required dictionary of input files for snpeff rules
Account for different 'layout's in sampletable
Updated the Snakefile to annotate and filter the VCF using the gnomAD database of variants and their associated allele frequencies, which for now has a hardcoded cutoff of .1
Make a few changes to the tests and clean up some things in the Snakfile to get the variant calling workflow ready to be merged into the master lcdb-wf branch
unclear if this is a CI-specific issue; the only problematic URL is ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gtf.gz which seems to work fine locally.
We've decided that the annotation steps are best left as a 'downstream' kind of task since 1) There are always so many problems with downloading databases and 2) The existing annotations were only built for human samples, which we want to avoid in lcdb-wf. Therefore we've taken out the annotation rules and code from `workflows/variant-calling/Snakefile`
variant calling workflow + testing
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Merged in the variant-calling workflow (#371), including substantial fixes to the test infrastructure.