Merge pull request #328 from nf-core/fix-convert-depths-gzip

Fix convert depths gzip
nf-core · Aug 25, 2022 · 6d26d5e · 6d26d5e
2 parents b7d6940 + 1414141
commit 6d26d5e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#329](https://github.com/nf-core/mag/pull/329) Each sample now gets it's own result directory for PyDamage analysis and filter
+- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module
+- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter
 
 ### `Dependencies`
 

diff --git a/modules/local/convert_depths.nf b/modules/local/convert_depths.nf
@@ -17,7 +17,7 @@ process CONVERT_DEPTHS {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    gunzip $depth
+    gunzip -f $depth
     bioawk -t '{ { if (NR > 1) { { print \$1, \$3 } } } }' ${depth.toString() - '.gz'} > ${prefix}_mb2_depth.txt
 
     cat <<-END_VERSIONS > versions.yml