Local running and testing of tools

When the user finishes making the tool (how to build a tool), you may need to simply test whether the tool can run normally. At this time, you need to pull the tool image first, and then configure the run.ini file. The content of run.ini is as follows.

[input]
fq1 = test_fq1.gz
fq2 = test_fq2.gz
[output]
cleanfq1 = out1.fq.gz
cleanfq2 = out2.fq.gz

Please note that the content in [input] is different in different tools. This is displayed according to the port field when the tool is created. This is just a demonstration of the fastp tool.

The tool details in FlowHub are shown in the figure below. For how to configure the command line, command line parameters, input and output in the tool, please refer to the document of ‘How to make a tool’.

You need to specify the input file in each port of [input] (the absolute path is required), and definite the directory where the result file is output after the tool is run in [output] (the absolute path is required), the reference content is as follows.

[input]
fq1 = "/demo_tool/test_data/test_fq1.gz"
fq2 = "/demo_tool/test_data/test_fq2.gz"

[output]
cleanfq1 = "/demo_tool/test_data/cleanfq1/out1.fq.gz"
cleanfq2 = "/demo_tool/test_data/cleanfq2/out2.fq.gz"

After the configuration is complete, you can use the following command to complete the test/run of the tool.

# note: fkit run [tool name: version number] [tool configuration file run.ini]
./fkit run demo:1 run.ini

After the operation is successful, the outDir folder will be generated in the /demo_tool/test_data/ directory, and the output result file will be under outDir. Other tools can be referred to for the same reason.