fix: sort BAM/BAI inputs to Manta for deterministic sample order

Author: Story Benjamin

CHANGELOG.md

@@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- Ensure deterministic sample ordering in Manta SV output by sorting BAM/BAI channel inputs [#815](https://github.com/nf-core/raredisease/pull/815)
 - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714)
 - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733)
 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745)

subworkflows/local/call_sv_manta/main.nf

@@ -16,11 +16,13 @@ workflow CALL_SV_MANTA {
         val_analysis_type // string: "wes", "wgs", or "mito"
 
     main:
-        ch_bam.collect{_meta, bam -> bam}
+        ch_bam.map{ _meta, bam -> bam }
+            .collect(sort: { a, b -> a.getName() <=> b.getName() })
             .toList()
             .set { bam_file_list }
 
-        ch_bai.collect{_meta, bai -> bai}
+        ch_bai.map{ _meta, bai -> bai }
+            .collect(sort: { a, b -> a.getName() <=> b.getName() })
             .toList()
             .set { bai_file_list }