diff --git a/spim_registration/timelapse/README.md b/spim_registration/timelapse/README.md index f830c0316199f15b2f88285adac21851dffe013b..60bc9d8075256eb072c82406a84aeb69fd14c2c4 100644 --- a/spim_registration/timelapse/README.md +++ b/spim_registration/timelapse/README.md @@ -106,6 +106,19 @@ If not: ```bash snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra}" ``` + +For error and output of the cluser add -o test.out -e test.err e.g.: +DRMAA +```bash +snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra} -o test.out -e test.err" +``` +LSF +```bash +snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra} -o test.out -e test.err" +``` + +Note: with this all the error and output files of one job would be written into these files. + Log files and supervision of the pipeline --------------- @@ -115,3 +128,5 @@ The log files are ordered according to their position in the workflow. Multiple force certain rules: use the -R flag to rerun a particular rule and everything downstream -R <name of rule> + +