Merge pull request #137 from mskcc/bugfix/sort_meta_map_values

sort read_group and fastq_pair_id values before concatenation
mskcc · Feb 3, 2025 · be76669 · be76669
2 parents c3b1e72 + 80af011
commit be76669
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#132](https://github.com/mskcc/forte/pull/132) - fix generate cff split/span logic for fusioncatcher and arriba
 
+- [#135](https://github.com/mskcc/forte/pull/135) - sort read_group and fastq_pair_id values before concatenation
+
 ### `Dependencies`
 
 ### `Deprecated`

diff --git a/subworkflows/local/group_reads.nf b/subworkflows/local/group_reads.nf
@@ -14,7 +14,7 @@ workflow GROUP_READS {
             [groupKey(meta_clone,meta.fq_num), reads, read_group, fastq_pair_id]
         }.groupTuple(by:[0])
         .map{ meta, reads, read_group, fastq_pair_id ->
-            meta = meta + [read_group:read_group.join(','), fastq_pair_id:fastq_pair_id.join(',')]
+            meta = meta + [read_group:read_group.sort().join(','), fastq_pair_id:fastq_pair_id.sort().join(',')]
             [meta, reads.flatten()]
         }