Merge pull request #29 from FertigLab/28-update-spacemarkers-to-call-…

…pairwise-pattern-comparisons 28 update spacemarkers to call pairwise pattern comparisons
FertigLab · Aug 14, 2024 · 275757d · 275757d
2 parents 1cde9bc + 6b6b5c5
commit 275757d
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/modules/local/spacemarkers.nf b/modules/local/spacemarkers.nf
@@ -1,7 +1,7 @@
 process SPACEMARKERS {
   tag "$meta.id"
-  label 'process_medium'
-  container 'ghcr.io/fertiglab/spacemarkers:1.1.1'
+  label 'process_high_memory'
+  container 'ghcr.io/fertiglab/spacemarkers:1.1.2.3'
 
   input:
     tuple val(meta), path(cogapsResult), path(data)
@@ -51,11 +51,12 @@ process SPACEMARKERS {
       saveRDS(optParams, file = "${prefix}/optParams.rds");
 
       #find genes that are differentially expressed in spatial patterns
-      spaceMarkers <- getInteractingGenes(data = dataMatrix, \
-                                          optParams = optParams, \
-                                          spPatterns = spPatterns, \
-                                          refPattern = "Pattern_1", \
-                                          mode = "DE", analysis="enrichment");
+      spaceMarkers <- getPairwiseInteractingGenes(data = dataMatrix, \
+                                                  optParams = optParams, \
+                                                  spPatterns = spPatterns, \
+                                                  mode = "DE", \
+                                                  analysis="enrichment");
+
       saveRDS(spaceMarkers, file = "${prefix}/spaceMarkers.rds");
                 '
     cat <<-END_VERSIONS > versions.yml
@@ -64,4 +65,4 @@ process SPACEMARKERS {
         R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
     END_VERSIONS
     """
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -10,7 +10,7 @@ params {
     distributed = '"genome-wide"'
 
     max_memory = '128.GB'
-    max_cpus = 1
+    max_cpus = 8
     max_time = '48.h'
 }
 
@@ -136,7 +136,6 @@ process {
 profiles {
     docker {
         docker.enabled         = true
-        docker.userEmulation   = true
     }
 
     singularity {