From d6d7d341ec26b06e1ec5221e6117cb5c85ee10f5 Mon Sep 17 00:00:00 2001 From: Maurizio Salvatore Podda Date: Thu, 23 May 2024 10:08:31 +0200 Subject: [PATCH] test R --- workflow/snakefile_final.smk | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflow/snakefile_final.smk b/workflow/snakefile_final.smk index cb1f4fe..7ad49ac 100755 --- a/workflow/snakefile_final.smk +++ b/workflow/snakefile_final.smk @@ -402,8 +402,8 @@ rule polyA_r_script: output: polyA_204 = config['datadirs']['r'] + "polyA_filtered_3UTR204.csv", polyA_220 = config['datadirs']['r'] + "polyA_filtered_3UTR220.csv" - script: - "{params.r_polya}" + shell: + "Rscript {params.r_polya}" ## Plot the ratio boxplot rule custom_r_script: @@ -412,8 +412,8 @@ rule custom_r_script: r_custom = config['scripts']['r_custom'] output: boxplot_custom = config['datadirs']['r'] + "ratio_BRAF.pdf" - script: - "{params.r_custom}" + shell: + "Rscript {params.r_custom}" ## Plot the pie charts and the ratio boxplot rule salmon_r_script: @@ -424,5 +424,5 @@ rule salmon_r_script: boxplot_salmon = config['datadirs']['r'] + "ratio_salmon.pdf", piecharts_salmon = config['datadirs']['r'] + "pie_charts.pdf", total_salmon = config['datadirs']['r'] + "total_salmon.pdf" - script: - "{params.r_salmon}" + shell: + "Rscript {params.r_salmon}"