Merge pull request #103 from Plant-Food-Research-Open/fix/plotsr

Fixed PLOTSR tokenize bug
Plant-Food-Research-Open · Jul 19, 2024 · 2cdeda3 · 2cdeda3
2 parents cf49135 + 2abbba5
commit 2cdeda3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,7 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
 3. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
 4. Now NCBI FCS GX module uses all the cores available from the Nextflow task
-5. Changed default branch name from `master` to `main` in nf-core template files
+5. Fixed a bug which caused `PLOTSR` to fail for certain assembly names [#102](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/102)
+6. Changed default branch name from `master` to `main` in nf-core template files
 
 ### `Dependencies`
 

diff --git a/subworkflows/local/fasta_synteny.nf b/subworkflows/local/fasta_synteny.nf
@@ -342,7 +342,7 @@ workflow FASTA_SYNTENY {
                                         | groupTuple
                                         | map { meta, syri, fastas ->
                                             def fasta_list          = fastas.flatten()
-                                            def syri_tags           = syri.collect { it.name.replace('syri.out', '').tokenize('.on.') }.flatten().unique()
+                                            def syri_tags           = syri.collect { it.name.replace('syri.out', '').split(/\.on\./).toList() }.flatten().unique()
                                             def proposed_order      = plotsr_assembly_order ? plotsr_assembly_order.tokenize(' ') : syri_tags.sort(false)
 
                                             def available_tags      = []