nf-core/airrflow: v4.2.0 Evanesco

Published December 11, 2024 | Version 4.2.0

Software Open

#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.

#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.

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | enchantr | 0.1.16 | 0.1.19 | | presto | 0.7.1 | 0.7.2 |

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.

Files

Name	Size	Download all
nf-core/airrflow-4.2.0.zip md5:bf1492b69f9b94dc91aa4e0c81847a05	3.3 MB	Preview Download

Is supplement to: Software: https://github.com/nf-core/airrflow/tree/4.2.0 (URL)