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| # Some common Data Workflows | |
| * Most workflows are implemented as Shell scripts (bash) for the ease of use and modification. | |
| [How Standards Proliferate](https://xkcd.com/927/) | |
| ## 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](misc/WGBS-RRBS_Potential_issues_with_custom_genomes.md) - 11/2022 |