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Feature/255 freemuxlet generic inputs #330
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- backwards-compatible change to add optional barcode_tag param - aertslab/popscle_helper_tools/issues/6
- Separate functions to take in data from getDataChannel and get the bam and barcodes files for the cellranger-style data - For bam,tsv input, join these dataChannels together on sampleId - Automatically handle multiple input types from getDataChannel and these can be run simultaneously - Resolves #255
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This allows multiple input formats for popscle (freemuxlet/demuxlet).
When using the
getDataChannelmethod to import data (specified with e.g.-profile cellranger_mex), thedata_channel_to_bam_barcodesfunction is used, and can format any of the cellranger channels to a tuple of(sampleId, bam, barcodes.tsv).Input with a (non-cellranger) bam and barcodes.tsv is possible by using
-profile bam,tsv. Here, the bam and tsv channels are joined on the sampleId key. A new parameterbarcode_tagallows specification of a different tag than the defaultCB.When using a workflow that first runs cellranger, the cellranger outputs don't include the full set of values that
getDataChannelproduces (type, format, group), but these can be assumed and handled by theget_bam_barcodes_from_cellranger_[rna|atac|arc]functions.