Change pwd info to results dir.

run_pipeline.sh

@@ -111,9 +111,10 @@ kilobytes_tot=$(mawk '$1 == "MemTotal:" {print $2}' /proc/meminfo)
 # to avoid pretending that we have all this memory available for snakemake rules.
 megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc)
 
+from_dir=$(pwd)
 #cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
 # TODO: check that this works
-cmd="(cd ${output_dir}; echo ${USER}@${HOSTNAME}:$(pwd) > pwd.txt; snakemake -s ${snakefile_base} --configfile ${config_base} --rulegraph | dot -Tpdf > rulegraph.pdf; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
+cmd="(cd ${output_dir}; echo ${USER}@${HOSTNAME}:${from_dir}/${output_dir} > pwd.txt; 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