commit new test salmon

mspodda · May 27, 2024 · 93a492e · 93a492e
1 parent 282e31c
commit 93a492e
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -31,7 +31,7 @@ jobs:
         run: |
            gzip -d test_data/chr7.fa.gz
       - name: Run snakemake
-        run: snakemake -s workflow/snakefile_final.smk --use-conda --rerun-incomplete --core 2 -k -P
+        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:

diff --git a/workflow/R/config_all.R b/workflow/R/config_all.R
@@ -21,7 +21,8 @@ BRAF_ids <- c("ENST00000288602.11","ENST00000469930.2","ENST00000479537.6","ENST
 
 ## libraries
 my_packages <- c("dplyr","ggplot2","tidyr","ggsignif","ggpubr","patchwork","stringr",
-                 "ggrepel","bedtoolsr","tibble")
+                 "ggrepel","bedtoolsr","tibble","GenomicAlignments","bioconductor-tximeta",
+                 "bioconductor-tximport")
 
 ## Sample typologies
 samples_typologies <-  c("lung_geo")