minor changes

saeyslab · Dec 12, 2023 · b6c3a9a · b6c3a9a
1 parent c8ac850
commit b6c3a9a
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -169,7 +169,7 @@ profiles {
 
         // Script parameters
         params {
-            rootdir = "$VSC_DATA/spotless-benchmark"
+            rootdir = "$VSC_DATA_VO_USER/spotless-benchmark"
             outdir = [props: "${params.rootdir}/deconv_proportions",
                       metrics: "${params.rootdir}/results",
                       synthspot: "${params.rootdir}/synthetic_data/"]

diff --git a/standards/standard.config b/standards/standard.config
@@ -2,11 +2,11 @@ params {
     file_type = 'rds'
 
     // If there is a hyphen, we only run one scenario (and for sc_input only get number before hyphen)
-    // If there is no hyphen, run all eight scenarios at once
+    // If there is no hyphen, run all scenarios at once
     sc_input = (params.standard =~ /-/ ? "standards/reference/${params.standard.split('-')[0]}*.${params.file_type}" :
                                          "standards/reference/${params.standard}*.${params.file_type}")
     sp_input = (params.standard =~ /(-|gold)/ ? "standards/$params.standard/*.${params.file_type}" :
-                                                "standards/$params.standard-[0-9]/*.${params.file_type}")
+                                                "standards/$params.standard-*/*.${params.file_type}")
     annot = "celltype"
     sampleID = "none"
     skip_metrics = (file_type =~ /rds/ ? false : true)

diff --git a/subworkflows/deconvolution/stride/run_method.nf b/subworkflows/deconvolution/stride/run_method.nf
@@ -1,6 +1,7 @@
 process runSTRIDE {
     tag "stride_${sp_file_basename}"
     label "retry"
+    label "longer_time"
     container 'csangara/sp_stride:latest'
     echo true
 
@@ -52,6 +53,7 @@ process runSTRIDE {
 process buildSTRIDEModel {
     tag "stride_build_$tag_suffix"
     label "retry"
+    label "longer_time"
     container 'csangara/sp_stride:latest'
     echo true