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s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data
GNU General Public License v3.0
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Activate/deactivate modules dynamically upon command-line invokation #135

Closed TBradley27 closed 4 months ago

TBradley27 commented 4 months ago

Hello,

Firstly, thank you for the great tool

As discussed in the release notes for v0.11.6, not all modules are activated by default. In particular, the kmer module is not activated by default since v0.11.6

The current method for switching modules on or off is to edit the Configuration folder as described

One problem with this approach, is that it makes it difficult to dynamically switch modules on/off when using fastqc within a larger pipeline.

What would be helpful is if modules could be switched on/off at the command line using a command line option or flag

s-andrews commented 4 months ago

You can do this on the command line, but by the addition of a config file. If you create a local copy of the limits.txt file then use the --limits option to pass the modified config file and this will be used over the global version installed with the program. That way you can change the behaviour even if you don't have permission to edit the main configuration files. 

    -l              Specifies a non-default file which contains a set of criteria
    --limits        which will be used to determine the warn/error limits for the
                    various modules.  This file can also be used to selectively
                    remove some modules from the output all together.  The format
                    needs to mirror the default limits.txt file found in the
                    Configuration folder.
TBradley27 commented 4 months ago

My apologies for missing this. Thank you very much!