pigx
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BIMSBbioinfo
Pipelines in genomics
A detailed documentation for development which will track the most recent changes - i.e. when a .in file appears, that we know where it is used, and why, and that...
Develop a system without the .in files - i.e. have a local config/settings file which would define which filea need to be changed during the configuration steps (which would also...
The pipeline reads the .Renviron files in the current directory. This can mess up R dependencies.
By default the pipelines really shouldn't print all that much. We could filter the output and only print a progress report. Using terminal control codes we could do this on...
For the ChIPseq pipeline I had the feeling that the dag building took way too long for the dry-run (in total around 250 jobs), so I started searching a bit...
In some of the pipelines we already have some verbosity options included, see https://github.com/BIMSBbioinfo/pigx_bsseq/pull/107. Here we added the snakemake commands `--printshellcmds` and `--verbose` directly as arguments. As Rekado actually pointed...
Right all of us have the validate_input() call at the top of the Pipeline Scripts, such that Snakemake is already invoked, even though we do not know if we have...
Hi Guys, As an feature for advanced users I like to add the possibility to pass arguments to qsub other than the default ones. For this we need to adjust...
The code example `pigx rnaseq` is very short and somewhat anticlimatic, because it doesn't show any example output. Replace this with an animated gif of a short command line session...