Merge pull request #121 from Plant-Food-Research-Open/debug/mmc

Fixed multiple bin binds failure in ASSEMBLATHON_STATS
Plant-Food-Research-Open · Jul 31, 2024 · de3e6dc · de3e6dc
2 parents c5165fe + 4e86875
commit de3e6dc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,8 +24,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 5. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92)
 6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98)
 7. Now soft masked regions are unmasked before computing LAI [#117](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/117)
-8. Changed `NextFlow` to `Nextflow`
-9. Updated citation to Bioinformatics
+8. Fixed a bug in `ASSEMBLATHON_STATS` which caused it to fail on MMC executor due to multiple binds of the `bin` directory
+9. Changed `NextFlow` to `Nextflow`
+10. Updated citation to Bioinformatics
 
 ### `Dependencies`
 

diff --git a/modules/local/assemblathon_stats.nf b/modules/local/assemblathon_stats.nf
@@ -28,7 +28,7 @@ process ASSEMBLATHON_STATS {
         | xargs
     )
 
-    falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm)"
+    falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm | head -n 1)"
 
     ln -s "\$falite_path" FAlite_a93cba2.pm
-Original file line number
+Diff line change
@@ Expand Up / @@ -28,7 +28,7 @@ process ASSEMBLATHON_STATS { @@
             | xargs
         )
-        falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm)"
+        falite_path="\$(find \$paths_to_check -name FAlite_a93cba2.pm | head -n 1)"
         ln -s "\$falite_path" FAlite_a93cba2.pm
@@ Expand Down @@