STAR: Add support for no/multiple whitelist files #488
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This PR adds support for complex barcode configurations possible with
--soloType CB_UMI_Complex
in STAR, where multiple barcode segments can occur at different positions (e.g.,--soloCBposition 0_7_0_13 0_16_0_23
) with separate whitelist files (--soloCBwhitelist whitelist1.txt whitelist2.txt
). See the STAR manual for reference.Previously, the pipeline only accepted a single whitelist file (optionally gzipped). This PR allows passing multiple whitelist files via
params.barcode_whitelist
as a comma-separated list.Additionally, this PR makes it possible to skip whitelist specification, which supports use cases where all barcodes should be accepted. Before, this caused a failure in modules/local/star_align.nf#L64 due to
$whitelist
evaluating to an empty string and the bash code failing.