:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
This would help make it easier to continue/restart failed or incomplete jobs.
To check if file exists:
FILE=/path/to/file.txt
if test -f "$FILE"; then
echo "$FILE exists."
fi
To check if folder exists:
FILE=/path/to/folder
if [ -d "$FILE" ]; then
echo "$FILE is a directory."
fi
For example, a large binReassemble job timed out after the 24 hr limit on my cluster. To continue the job without re-recruiting reads & re-reassembling some genomes I had to manually silence the cp command in the Snakefile rule. This could be handled automatically by a conditional statement as shown above, e.g. if tmp/$job/$sample exists then do not copy any new files into it.
This would help make it easier to continue/restart failed or incomplete jobs.
To check if file exists:
To check if folder exists:
For example, a large binReassemble job timed out after the 24 hr limit on my cluster. To continue the job without re-recruiting reads & re-reassembling some genomes I had to manually silence the cp command in the Snakefile rule. This could be handled automatically by a conditional statement as shown above, e.g. if tmp/$job/$sample exists then do not copy any new files into it.