test r bioconductor

mspodda · May 24, 2024 · 2034f77 · 2034f77
1 parent 5976a3b
commit 2034f77
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/workflow/envs/R.yml b/workflow/envs/R.yml
@@ -16,7 +16,6 @@ dependencies:
   - r-tibble
   - r-bedtoolsr
   - r-data.table
-
-##  - bioconductor-GenomicAlignments
-##  - bioconductor-tximeta
-##  - bioconductor-tximport
+  - bioconductor-GenomicAlignments
+  - bioconductor-tximeta
+  - bioconductor-tximport
diff --git a/workflow/snakefile_final.smk b/workflow/snakefile_final.smk
@@ -425,6 +425,7 @@ rule custom_r_script:
 ## Plot the pie charts and the ratio boxplot
 rule salmon_r_script:
     input:
+        salmon_sf =  config['datadirs']['salmon'] + "/{file}/"  + 'quant.sf'
     params:
         r_salmon = config['scripts']['r_salmon']
     output: