testint plot

mspodda · May 23, 2024 · 3af32dc · 3af32dc
1 parent 8fcca08
commit 3af32dc
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -32,5 +32,10 @@ jobs:
            gzip -d test_data/chr7.fa.gz
       - name: Run snakemake
         run: snakemake -s workflow/snakefile_final.smk --use-conda --rerun-incomplete --core 2 -k
+      - name: Upload plot as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: plot
+          path: workflow/R/ratio_BRAF.pdf
 
 
diff --git a/workflow/R/R_custom.R b/workflow/R/R_custom.R
@@ -1,5 +1,5 @@
 ### Create and load vector of packages
-setwd(final_output)
+#setwd(final_output)
 source("config_all.R")
 lapply(my_packages, require, character.only = TRUE) 
 
@@ -142,7 +142,7 @@ bp_ratios <- ggplot(db_ratio, aes(x=group, y=value, fill=group)) +
   xlab("Tissue Typology") 
 bp_ratios
 # Closing the graphical device
-setwd(final_output)
+#setwd(final_output)
 pdf("ratio_BRAF.pdf", width = 21.5,height = 11)
 bp_ratios
 dev.off()