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Vitek-Lab · Nov 12, 2024 · 10a796b · 10a796b
1 parent 054ccbb
commit 10a796b
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -45,8 +45,8 @@ jobs:
 
     - name: Fetch Output
       run: |
-        scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_output.txt job_output.txt
-        scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_error.txt job_error.txt
+        scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_output.txt job_output.txt
+        scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_error.txt job_error.txt
 
     - name: Upload Output as Artifact
       uses: actions/upload-artifact@v4

diff --git a/benchmark/benchmark.R b/benchmark/benchmark.R
@@ -123,11 +123,11 @@ data_process_tasks <- list(
   ),
   list(
     label = "Data process without Normalization",
-    result = function() dataProcess(msstats_format, normalization = "FALSE", n_top_feature = 20)
+    result = function() dataProcess(msstats_format, featureSubset = "topN", normalization = "FALSE", n_top_feature = 20)
   ),
   list(
     label = "Data process without Normalization with MBImpute False",
-    result = function() dataProcess(msstats_format, normalization = "FALSE", n_top_feature = 20, MBimpute = FALSE)
+    result = function() dataProcess(msstats_format, featureSubset = "topN", normalization = "FALSE", n_top_feature = 20, MBimpute = FALSE)
   )
 )
 

diff --git a/benchmark/config.slurm b/benchmark/config.slurm
@@ -1,7 +1,7 @@
 #!/bin/bash
 #SBATCH --job-name=msstats_benchmark_job
-#SBATCH --output=job_output.txt
-#SBATCH --error=job_error.txt
+#SBATCH --output=/work/VitekLab/Projects/Benchmarking/job_output.txt
+#SBATCH --error=/work/VitekLab/Projects/Benchmarking/job_error.txt
 #SBATCH --time=01:00:00         # Set the maximum run time
 #SBATCH --ntasks=1              # Number of tasks (one process)
 #SBATCH --cpus-per-task=8      # Use 8 CPU cores for the task