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docs/nf_customize/03_execution.md

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The [`nf-core/demo`](https://nf-co.re/demo/) pipeline consists of three processes:
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- ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)): Read quality control
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- ([`SEQTK_TRIM`](https://github.com/lh3/seqtk)): Trim low quality bases from FastQ files
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- ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)): Read quality control
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- ([`SEQTK_TRIM`](https://github.com/lh3/seqtk)): Trim low quality bases from FASTQ files
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- ([`MULTIQC`](http://multiqc.info/)): Present quality control reports for raw reads
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[`nf-core/demo`](https://nf-co.re/demo/) takes a samplesheet that contains paths to FASTQ files as an input and will produce four output folders with logs and reports:

docs/nf_customize/04_config.md

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While some of these files are already included in the nf-core pipeline repository (e.g., the `nextflow.config` file in the nf-core pipeline repository), some are automatically identified on your local system (e.g., the `nextflow.config` in the launch directory), and others are only included if they are specified using `run` options (e.g., `-params-file`, and `-c`).
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Understanding how and when these files are interpreted by Nextflow is critical for the accurate configuration of a pipelines execution.
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Understanding how and when these files are interpreted by Nextflow is critical for the accurate configuration of a pipeline execution.
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## Parameters
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Scopes allow you to quickly configure settings required to deploy a pipeline on different infrastructure using different software management.
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For example, the `executor` scope can be used to provide settings for the deployment of a pipeline on a HPC cluster. Similarly, the `singularity` scope controls how Singularity containers are executed by Nextflow.
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For example, the `executor` scope can be used to provide settings for the deployment of a pipeline on an HPC cluster. Similarly, the `singularity` scope controls how Singularity containers are executed by Nextflow.
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A common scenario is for users to write a custom configuration file specific to running a pipeline on their infrastructure.
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While some tool arguments are included as a part of a module. To make nf-core modules sharable across pipelines, most tool arguments are defined in the `conf/modules.conf` file in the pipeline code under the `ext.args` entry.
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Importantly, having these arguments outside of the module also allows them to be customized at runtime.
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Importantly, having these arguments outside the module also allows them to be customized at runtime.
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For example, if you wanted to add arguments to the `MULTIQC` process in the `nf-core/demo` pipeline, you could use the process scope and the `withName` selector:
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