Merge pull request #359 from noecochetel/master

Fix expansion of ignore_r1 parameters in modules.config
nf-core · Nov 6, 2023 · 7ec570c · 7ec570c
2 parents bc60097 + f981cbf
commit 7ec570c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Bug fixes & refactoring
 
 - 🛠 Copy methylKit-compatible files to publishDir [#357](https://github.com/nf-core/methylseq/pull/357)
+- 🐛 fix `ignore_r1` and `ignore_3prime_r1` variable expansion [#359](https://github.com/nf-core/methylseq/pull/359)
 
 ## [v2.5.0](https://github.com/nf-core/methylseq/releases/tag/2.5.0) - 2023-10-18
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -209,8 +209,8 @@ process {
             params.comprehensive   ? ' --comprehensive --merge_non_CpG' : '',
             params.meth_cutoff     ? " --cutoff ${params.meth_cutoff}" : '',
             params.nomeseq         ? '--CX' : '',
-            params.ignore_r1 > 0   ? '--ignore ${params.ignore_r1}' : '',
-            params.ignore_3prime_r1 > 0   ? '--ignore_3prime ${params.ignore_3prime_r1}' : '',
+            params.ignore_r1 > 0   ? "--ignore ${params.ignore_r1}" : '',
+            params.ignore_3prime_r1 > 0   ? "--ignore_3prime ${params.ignore_3prime_r1}" : '',
             meta.single_end ? '' : (params.no_overlap           ? ' --no_overlap'                         : '--include_overlap'),
             meta.single_end ? '' : (params.ignore_r2        > 0 ? "--ignore_r2 ${params.ignore_r2}"       : ""),
             meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "")