Releases 4.2.0
Added
#334 Added TRUST4 support.#344 Added option to remove V and C primer region when sequence is unknown.#344 Added option to save non-productive sequences#344 Allow for maskprimers align with UMI on both V gene and C gene primers.#344 Update pipeline template to nf-core tools v3.0.2.357 Deprecate isotype_column parameter in favor of annotating C region from internal c_region alignment or c_primer alignment into the c_call column.
Fixed
#344 Avoid saving pRESTO intermediate fastq files in results directory.#344 Simplified pRESTO Maskprimers score and Maskprimers extract processes.#344 Fix clustersets approach, consider both reads clusters annotation.#344 Allow for partial alignments in MakeDB for mouse TCR data, to bypass junction check for TRAV germlines with additional positions (e.g. 84A).#344 Fix parse logs merging dataframes using pandas join to produce logs even when there are failing samples.#344 Use pRESTO Collapseseq with n=0 by default due to runtime issues.
Dependencies
Dependency
Old version
New version
enchantr
0.1.16
0.1.19
presto
0.7.1
0.7.2
Deprecated parameters
isotype_column: if c_call column value is NA, now c_region and c_primer column values respectively are annotated into the c_call column.
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