WIP swiftseq demux integration #600
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add `collapse_duplicated_barcodes` input param to `illumina_demux` task, which will be passed to `illumina.py illumina_demux`, and will toggle collapsing of duplicated barcodes or barcode pairs, allowing picard to run IlluminaBaseCallsToSam without the errors that would normally be raised if the sample sheet provided has dups. This new param is set to false by default, so as to not change expected behavior of pipelines currently using the task.
…x task, if collapse_duplicated_barcodes=true
…`rev_comp_barcodes_before_demux` input arguments illumina_demux task: expose new `rev_comp_barcodes_before_demux` and `rev_comp_barcodes_before_demux` input arguments to allow the user to toggle rev-comp of sample sheet barcodes, and optionally supply a list of columns that should be rev-comped (default of `["barcode_2"]`).
…rocess that produced the numbers
…L validation fixes; allow optional flowcell_dir_path String to be passed in as alternative to flowcell_tgz; WDL CI script improvements illumina_demux docker image is pinned to '2.4.1-21-g4f968929-ct-swiftseq-demux-integration' on this branch (for now); remove cruft (unused param meta); WDL validation fixes; allow optional flowcell_dir_path String to be passed in as alternative to flowcell_tgz; WDL CI script improvements
…rd glob expression as string literal in the event the expansion does not exist
…code position, or at read ends before inner barcode demux)
… to illumina.py::illumina_demux call
change default docker image on dev branch of this repo to more recent build on dev branch of viral-core
…s that cannot be determined); bash lint fix in brace groups (add missing semicolon terminator); quote some paths in a few places
…s to match requirements-modules.txt
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