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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.

@LeonHafner LeonHafner self-assigned this Aug 4, 2025
@LeonHafner LeonHafner added the enhancement New feature or request label Aug 4, 2025
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I just saw that #486 also adds support for running without a whitelist file That PR appeared after I had already started working on this, sorry for the duplication. However, to fully support the CB_UMI_Complex mode, it would still be very useful to add support for multiple whitelist files.

@grst grst mentioned this pull request Aug 5, 2025
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