Cannot use qvalue when call peaks with MACS2

[lingyunsong]

Describe the bug

Hi, MACS2 peak calls usually have two optional threshold: p values and q values. In the encode atacseq pipeline there is only one option: pvalue-threshold at the step of peak calling.
We need qvalues = 0.01 as threshold. I revised the "pvalue-threshold" to "q" in the module "encode_task_macs2_atac.py" but it did not change the output. It was still pvalue. Could you give comments on how to run the pipeline with q value setting on MACS2 peak calling?

OS/Platform

• OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
• Conda version: If you used Conda ($ conda --version).
• Pipeline version: [e.g. v1.8.0]
• Caper version: [e.g. v1.2.0]

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Input JSON file

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Troubleshooting result

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