flash

The FLASh module parses the log messages generated by the FLASh read merger. To create a log file, you can use tee. From the FLASh help:

flash reads_1.fq reads_2.fq 2>&1 | tee logfilename.log

The sample name is set by the first input filename listed in the log. However, this can be changed to using the first output filename (i.e. if you used FLASh's --output-prefix=PREFIX option) by using the following config:

flash:
  use_output_name: true

The module can also parse the .hist numeric histograms output by FLASh.

Note that the histogram's file format and extension are too generic by themselves which could result in the accidental parsing a file output by another tool. To get around this, the MultiQC module only parses files with the filename pattern *flash*.hist.

To customise this (for example, enabling for any file ending in *.hist), use the following config change:

sp:
  flash/hist:
    fn: "*.hist"