'make_fastqs': apply index filter options to Cellranger

fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.

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'make_fastqs': apply index filter options to Cellranger #936

Closed pjbriggs closed 5 months ago

pjbriggs commented 5 months ago

Updates the handling of the tenx_filter_single_index and tenx_filter_dual_index options (which can be specified in the make_fastqs command via the --lanes option) so that they will also be applied to cellranger mkfastq (previously they were only exposed for cellranger-arc).

These options may be useful in certain special cases, see e.g. https://kb.10xgenomics.com/hc/en-us/articles/115003082371