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Changes from code review from @mashehu
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docs/usage.md

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<!-- /TOC -->
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# Introduction
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## Running the pipeline
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### Quick Start

nextflow_schema.json

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"help_text": "Turns off QualiMap and thus does not compute coverage and other mapping metrics.\n"
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}
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},
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"fa_icon": "fas fa-forward",
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"fa_icon": "fas fa-fast-forward",
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"help_text": "Some of the steps in the pipeline can be executed optionally. If you specify\nspecific steps to be skipped, there won't be any output related to these\nmodules."
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},
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"complexity_filtering": {

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