Changes between Version 3 and Version 4 of SOPs/nextflow
- Timestamp:
- 03/26/25 15:40:32 (9 days ago)
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SOPs/nextflow
v3 v4 69 69 To run a pipeline: 70 70 71 1. Choose a pipeline to run. See the available nf-core pipelines. If you have nf-core tools installed, run 72 {{{ 73 nf-core pipelines list 74 }}} 75 76 77 2. Configure Nextflow to run on your system: 71 1. Configure Nextflow to run on your system: 78 72 79 73 The simplest way to run is with -profile docker (or singularity). This instructs Nextflow to execute jobs locally, with Docker (or Singularity) to fulfill software dependencies. … … 84 78 85 79 86 3. Run the tests for your pipeline in the terminal to confirm everything is working:80 2. Run the tests for your pipeline in the terminal to confirm everything is working: 87 81 88 82 … … 96 90 97 91 98 4. Read the pipeline documentation to see which command-line parameters are required. This will be specific to your data type and usage.92 3. Read the pipeline documentation to see which command-line parameters are required. This will be specific to your data type and usage. 99 93 100 5. To launch the pipeline with real data, omit the test config profile and provide the required pipeline-specific parameters. For example, to run the CUTandRun pipeline, your command will be similar to this:94 4. To launch the pipeline with real data, omit the test config profile and provide the required pipeline-specific parameters. For example, to run the CUTandRun pipeline, your command will be similar to this: 101 95 102 96 … … 110 104 }}} 111 105 112 6. Once complete, check the pipeline execution and quality control reports (such as multiqc_report.html files for MultiQC reports). Each pipeline’s documentation describes the outputs to expect.106 5. Once complete, check the pipeline execution and quality control reports (such as multiqc_report.html files for MultiQC reports). Each pipeline’s documentation describes the outputs to expect. 113 107 114 108 Please refer to nf-core documentation for more details (https://nf-co.re/docs/usage/getting_started/introduction).
