added -o param to script

nf-core · Jul 30, 2024 · 05ddd5a · 05ddd5a
1 parent 08cfac4
commit 05ddd5a
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/modules/nf-core/gmmdemux/main.nf b/modules/nf-core/gmmdemux/main.nf
@@ -46,7 +46,8 @@ process GMMDEMUX {
         $skip \\
         $examine_cells \\
         $hto_matrix \\
-        $hto_names
+        $hto_names \\
+        -o .
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         GMM-Demux: $VERSION

diff --git a/modules/nf-core/gmmdemux/tests/nextflow.config b/modules/nf-core/gmmdemux/tests/nextflow.config
@@ -11,6 +11,6 @@ params{
 process {
 
     withName: GMMDEMUX {
-        ext.args = "-t ${params.threshold} -o . --summary ${params.num_cells} -a ${params.ambiguous} "
+        ext.args = "-t ${params.threshold} --summary ${params.num_cells} -a ${params.ambiguous} "
     }
 }