qbicsoftware-archive / qcprot

Quality control for mass spec proteomics

Run a quality control workflow on mzML files from mass spec based proteomics.

Requirements

• A python 3 environment with (eg. anaconda)
  • snakemake
  • jinja2
  • qproject (eg. pip install git+https://github.com/qbicsoftware/qproject)
  • xtandem
  • R
• openms 2.0 (there is a conda package that can be installed with conda install -c aseyboldt openms that might or might not work)

##Usage Create the directory structure of the workdir (it should not exist):

qproject create -t path/to/workdir -w github:qbicsoftware/qcprot

This will create the <workdir> and some directories inside and clone qcprot to <workdir>/src. Copy the mzML files to <workdir>/data and your fasta file(s) to <workdir>/ref.

Copy the ini files to etc:

cd <workdir>/src/inis <workdir>/etc

and modify if necessary.

Execute the workflow with

cd <workdir>/src
snakemake

You can also adjust the jobscript and use qproject to execute the workflow:

qproject run -t <workdir>

If qproject is used to execute qcprot some data about the run is stored in <workdir>/archive for reproducibility. This is still very much work in progress though' The output of snakemake will end up in <workdir>/logs/snake.err.