Some common Data Workflows

• Most workflows are implemented as Shell scripts (bash) for the ease of use and modification.

How Standards Proliferate

Changes

• [2021-07] Due to I/O issues I modified all workflows to use MXQ_JOB_TMPDIR as temporary storage location. Especially GATK, FastQC and also macs2 are very I/O hungry .. In order to use MXQ_JOB_TMPDIR it is important to specify --tmpdir nnG when submitting cluster jobs with mxqsub. For this I also put some example submission scripts to the respective workflow directory. https://intranet.molgen.mpg.de/de/service/scientific-service/it/it-news/mxq-cluster-new-feature-tmpdir/

Problems / Issues

• WGBS/RRBS: mcall failure with non-standard genome references - 11/2022