Added seed parameters for AUCell step

- Resolves #13
vib-singlecell-nf · Feb 28, 2020 · 73a57d8 · 73a57d8
1 parent 999a1a1
commit 73a57d8
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diff --git a/processes/aucell.nf b/processes/aucell.nf
@@ -40,13 +40,15 @@ process AUCELL {
                 throw new Exception("walltime is missing in params.sc.scenic.aucell")
         }
         outputFileName = "numRuns" in toolParams && toolParams.numRuns > 1 ? sampleId + "__run_" + runId +"__auc_" + type + ".loom": sampleId + "__auc_" + type + ".loom"
+        seed = "numRuns" in toolParams && toolParams.numRuns > 1 ? (params.seed + runId) : params.seed
         """
         pyscenic aucell \
             $filteredLoom \
             $regulons \
             -o "${outputFileName}" \
             --cell_id_attribute ${toolParams.cell_id_attribute} \
             --gene_attribute ${toolParams.gene_attribute} \
+            --seed ${seed} \
             --num_workers ${processParams.numWorkers}
         """
 

diff --git a/scenic.config b/scenic.config
@@ -21,7 +21,6 @@ params {
             gene_attribute = 'Gene'
             grn {
                 algorithm = 'grnboost2' // also available: 'genie3'
-                seed = ''
                 // cluster options:
                 pmem = '2gb'
                 maxForks = 1