Generate a rulegraph for each run.

run_pipeline.sh

@@ -98,7 +98,7 @@ megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc)
 
 #cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
 # TODO: check that this works
-cmd="(cd ${output_dir}; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
+cmd="(cd ${output_dir}; snakemake -s ${snakefile_base} --configfile ${config_base} --rulegraph | dot -Tpdf > rulegraph.pdf; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
 
 echo ${cmd} | tee -a ${log_base}.log
 # https://unix.stackexchange.com/a/245610/55127

singularity/run_pipeline.def

@@ -36,6 +36,8 @@ From:python:3.7-buster
 	apt-get -y update
 	# Useful for interactive work using the container
 	apt-get -y install vim
+	# To be able to generate rule graphs of the workflows
+	apt-get -y install graphviz
 	# run_pipeline.sh (and maybe other tools) needs bc
 	apt-get -y install bc rsync
 	apt-get -y install bedops bedtools bowtie2 cutadapt subread hisat2 parallel samtools