Use seed for nondeterministic processes vib-singlecell-nf/vsn-pipelin…

…es#43
vib-singlecell-nf · Feb 14, 2020 · 326387d · 326387d
1 parent 0a60761
commit 326387d
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/bin/run_pca_cv.R b/bin/run_pca_cv.R
@@ -131,15 +131,21 @@ RunPCACV <- function(
   to = 150,
   by = 5,
   maxit = 200,
-  seed = 617,
+  seed = NULL,
   n.cores = 1,
   verbose = T,
   default.svd = F) {
-  set.seed(seed)
+  # Required by irlba::irlba for reproducibility
+  if(!is.null(seed)) {
+    set.seed(seed)
+  } else {
+    warnings("No seed is set!")
+  }
   library(foreach)
   library(doMC)
   registerDoMC(cores = n.cores) 
   library(irlba)
+
   if(default.svd) {
     print("Default SVD is using for estimating the number PCs.") 
   }

diff --git a/processes/runPCACV.nf b/processes/runPCACV.nf
@@ -25,13 +25,13 @@ process PCACV__FIND_OPTIMAL_NPCS {
         """
         ${binDir}run_pca_cv.R \
             --input-file ${f} \
+            ${'--seed ' + (params.global.containsKey('seed') ? params.global.seed: params.seed)} \
             ${(processParams.containsKey('accessor')) ? '--accessor "' + processParams.accessor.replace('$','\\$') + '"': ''} \
             ${(processParams.containsKey('kFold')) ? '--k-fold ' + processParams.libraries: ''} \
 			${(processParams.containsKey('fromNPC')) ? '--from-n-pc ' + processParams.fromNPC: ''} \
 			${(processParams.containsKey('toNPC')) ? '--to-n-pc ' + processParams.toNPC: ''} \
 			${(processParams.containsKey('byNPC')) ? '--by-n-pc ' + processParams.byNPC: ''} \
             ${(processParams.containsKey('maxIters')) ? '--max-iters ' + processParams.libraries: ''} \
-			${(processParams.containsKey('seed')) ? '--seed ' + processParams.fromNPC: ''} \
 			${(processParams.containsKey('nCores')) ? '--n-cores ' + processParams.nCores: ''} \
 			${(processParams.containsKey('defaultSVD')) ? '--default-svd ' + processParams.defaultSVD: ''} \
             ${(processParams.containsKey('verbose')) ? '--verbose ' + processParams.verbose: ''} \