makedb partial for mouse TR

ggabernet · Sep 4, 2024 · 0b8fa48 · 0b8fa48
1 parent e106235
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Avoid saving pRESTO intermediate fastq files in results directory.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Simplified pRESTO Maskprimers score and Maskprimers extract processes.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Fix clustersets approach, consider both reads clusters annotation.
+- [#344](https://github.com/nf-core/airrflow/pull/344) Allow for partial alignments in MakeDB for mouse TCR data, to bypass junction check for TRAV germlines with additional positions (e.g. 84A).
 
 ### `Dependencies`
 

diff --git a/modules/local/changeo/changeo_makedb.nf b/modules/local/changeo/changeo_makedb.nf
@@ -21,10 +21,11 @@ process CHANGEO_MAKEDB {
 
     script:
     def args = task.ext.args ?: ''
+    def partial = meta.species.toLowerCase()=='mouse' && meta.locus.toLowerCase()=='tr'  ? '--partial' : ''
     """
     MakeDb.py igblast -i $igblast -s $reads -r \\
     ${reference_fasta}/${meta.species.toLowerCase()}/vdj/ \\
-    $args \\
+    $args $partial \\
     --outname ${meta.id} > ${meta.id}_makedb_command_log.txt
 
     cat <<-END_VERSIONS > versions.yml