Reimplement 'set_cell_count_from_project' function in QC pipeline - #1111
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Reimplement the 'set_cell_count_for_project' function to remove code for determining the 10x software package outputs should be parsed for cell counts; instead the name of the appropriate package must be explicitly supplied as an argument. Also updates the 'Set10xCellCount' task in the QC pipeline to accommodate the changes, and the invocations of the task within the pipeline.
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Reimplements the
set_cell_count_from_projectfunction in the QC pipeline utilitys module (qc/utils), to remove the code that attempted to automatically determine which 10x Genomics software pipeline outputs (e.g.cellranger,cellranger-atacetc) the cell counts should be extracted from. Instead the function now expects the package name to be explicitly specified as an argument.Supporting the automatic package determination code (which uses the project metadata to try and work out which package was used) has in the past meant that the function has been a weak point in the pipeline when adding new 10x Genomics platforms. Removing this functionality should help make the pipeline more robust and able to deal with new platforms without further updates, as long as they use one of the current standard software pipelines.
As part of the PR the
SetCellCountFromCellrangertask in the QC pipeline (qc/pipeline) has been renamed (toSet10xCellCount) and updated to accommodate the changes to theset_cell_count_from_projectfunction; in turn this has required very minor updates to theRunCellrangerCountandRunCellrangerMultitasks from thecellranger*_countandcellranger_multiQC modules (in order to make the 10x pipeline name available for input into theSet10xCellCounttask).