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Example.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="generator" content="Asciidoctor 2.0.16">
<title>Nextflow training</title>
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Open+Sans:300,300italic,400,400italic,600,600italic%7CNoto+Serif:400,400italic,700,700italic%7CDroid+Sans+Mono:400,700">
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<div id="header">
<h1>Nextflow training <span class="image right Seqera Labs Logo"><img src="img/seqera-logo-black.png" alt="Logo" width="300" height="100"></span></h1>
<div id="toc" class="toc2">
<div id="toctitle">Table of Contents</div>
<ul class="sectlevel0">
<li><a href="#_welcome_to_the_nextflow_training_camp">Welcome to the Nextflow Training Camp !</a></li>
<li><a href="#_the_plan">The Plan</a></li>
<li><a href="#_summary">Summary</a>
<ul class="sectlevel1">
<li><a href="#_environment_setup">1. Environment setup</a>
<ul class="sectlevel2">
<li><a href="#_requirements">1.1. Requirements</a></li>
<li><a href="#_training_material">1.2. Training material</a></li>
<li><a href="#_setup_aws_cloud9_environment_optional">1.3. Setup AWS Cloud9 environment (Optional)</a></li>
<li><a href="#_nextflow_installation">1.4. Nextflow installation</a></li>
</ul>
</li>
<li><a href="#_get_started_with_nextflow">2. Get started with Nextflow</a>
<ul class="sectlevel2">
<li><a href="#_basic_concepts">2.1. Basic concepts</a>
<ul class="sectlevel3">
<li><a href="#_processes_and_channels">2.1.1. Processes and channels</a></li>
<li><a href="#_execution_abstraction">2.1.2. Execution abstraction</a></li>
<li><a href="#_scripting_language">2.1.3. Scripting language</a></li>
</ul>
</li>
<li><a href="#_your_first_script">2.2. Your first script</a>
<ul class="sectlevel3">
<li><a href="#_nextflow_code_hello_nf">2.2.1. Nextflow code (hello.nf)</a></li>
<li><a href="#_in_detail">2.2.2. In detail</a></li>
<li><a href="#_in_dag_like_format">2.2.3. In DAG-like format</a></li>
</ul>
</li>
<li><a href="#_modify_and_resume">2.3. Modify and resume</a></li>
<li><a href="#_pipeline_parameters">2.4. Pipeline parameters</a></li>
</ul>
</li>
<li><a href="#_simple_rna_seq_pipeline">3. Simple Rna-Seq pipeline</a>
<ul class="sectlevel2">
<li><a href="#_define_the_pipeline_parameters">3.1. Define the pipeline parameters</a>
<ul class="sectlevel3">
<li><a href="#_exercise">3.1.1. Exercise</a></li>
<li><a href="#_exercise_2">3.1.2. Exercise</a></li>
<li><a href="#_recap">3.1.3. Recap</a></li>
</ul>
</li>
<li><a href="#_create_transcriptome_index_file">3.2. Create transcriptome index file</a>
<ul class="sectlevel3">
<li><a href="#_exercise_3">3.2.1. Exercise</a></li>
<li><a href="#_exercise_4">3.2.2. Exercise</a></li>
<li><a href="#_exercise_5">3.2.3. Exercise</a></li>
<li><a href="#_recap_2">3.2.4. Recap</a></li>
</ul>
</li>
<li><a href="#_collect_read_files_by_pairs">3.3. Collect read files by pairs</a>
<ul class="sectlevel3">
<li><a href="#_exercise_6">3.3.1. Exercise</a></li>
<li><a href="#_exercise_7">3.3.2. Exercise</a></li>
<li><a href="#_recap_3">3.3.3. Recap</a></li>
</ul>
</li>
<li><a href="#_perform_expression_quantification">3.4. Perform expression quantification</a>
<ul class="sectlevel3">
<li><a href="#_exercise_8">3.4.1. Exercise</a></li>
<li><a href="#_exercise_9">3.4.2. Exercise</a></li>
<li><a href="#_recap_4">3.4.3. Recap</a></li>
</ul>
</li>
<li><a href="#_quality_control">3.5. Quality control</a>
<ul class="sectlevel3">
<li><a href="#_exercise_10">3.5.1. Exercise</a></li>
<li><a href="#_recap_5">3.5.2. Recap</a></li>
</ul>
</li>
<li><a href="#_multiqc_report">3.6. MultiQC report</a>
<ul class="sectlevel3">
<li><a href="#_recap_6">3.6.1. Recap</a></li>
</ul>
</li>
<li><a href="#_handle_completion_event">3.7. Handle completion event</a></li>
<li><a href="#_bonus">3.8. Bonus!</a></li>
<li><a href="#_custom_scripts">3.9. Custom scripts</a>
<ul class="sectlevel3">
<li><a href="#_recap_7">3.9.1. Recap</a></li>
</ul>
</li>
<li><a href="#_metrics_and_reports">3.10. Metrics and reports</a></li>
<li><a href="#_run_a_project_from_github">3.11. Run a project from GitHub</a></li>
<li><a href="#_more_resources">3.12. More resources</a></li>
</ul>
</li>
<li><a href="#_manage_dependencies_containers">4. Manage dependencies & containers</a>
<ul class="sectlevel2">
<li><a href="#_docker_hands_on">4.1. Docker hands-on</a>
<ul class="sectlevel3">
<li><a href="#_run_a_container">4.1.1. Run a container</a></li>
<li><a href="#_pull_a_container">4.1.2. Pull a container</a></li>
<li><a href="#_run_a_container_in_interactive_mode">4.1.3. Run a container in interactive mode</a></li>
<li><a href="#_your_first_dockerfile">4.1.4. Your first Dockerfile</a></li>
<li><a href="#_build_the_image">4.1.5. Build the image</a></li>
<li><a href="#_add_a_software_package_to_the_image">4.1.6. Add a software package to the image</a></li>
<li><a href="#_run_salmon_in_the_container">4.1.7. Run Salmon in the container</a></li>
<li><a href="#_file_system_mounts">4.1.8. File system mounts</a></li>
<li><a href="#_upload_the_container_in_the_docker_hub_bonus">4.1.9. Upload the container in the Docker Hub (bonus)</a></li>
<li><a href="#_run_a_nextflow_script_using_a_docker_container">4.1.10. Run a Nextflow script using a Docker container</a></li>
</ul>
</li>
<li><a href="#_singularity">4.2. Singularity</a>
<ul class="sectlevel3">
<li><a href="#_create_a_singularity_images">4.2.1. Create a Singularity images</a></li>
<li><a href="#_running_a_container">4.2.2. Running a container</a></li>
<li><a href="#_import_a_docker_image">4.2.3. Import a Docker image</a></li>
<li><a href="#_run_a_nextflow_script_using_a_singularity_container">4.2.4. Run a Nextflow script using a Singularity container</a></li>
<li><a href="#_the_singularity_container_library">4.2.5. The Singularity Container Library</a></li>
</ul>
</li>
<li><a href="#_condabioconda_packages">4.3. Conda/Bioconda packages</a>
<ul class="sectlevel3">
<li><a href="#_bonus_exercise">4.3.1. Bonus Exercise</a></li>
</ul>
</li>
<li><a href="#_biocontainers">4.4. BioContainers</a></li>
<li><a href="#_more_resources_2">4.5. More resources</a></li>
</ul>
</li>
<li><a href="#_channels">5. Channels</a>
<ul class="sectlevel2">
<li><a href="#_channel_types">5.1. Channel types</a>
<ul class="sectlevel3">
<li><a href="#_queue_channel">5.1.1. Queue channel</a></li>
<li><a href="#_value_channels">5.1.2. Value channels</a></li>
</ul>
</li>
<li><a href="#_channel_factories">5.2. Channel factories</a>
<ul class="sectlevel3">
<li><a href="#_value">5.2.1. value</a></li>
<li><a href="#_from">5.2.2. from</a></li>
<li><a href="#_of">5.2.3. of</a></li>
<li><a href="#_fromlist">5.2.4. fromList</a></li>
<li><a href="#_frompath">5.2.5. fromPath</a></li>
<li><a href="#_fromfilepairs">5.2.6. fromFilePairs</a></li>
<li><a href="#_fromsra">5.2.7. fromSRA</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_processes">6. Processes</a>
<ul class="sectlevel2">
<li><a href="#_script">6.1. Script</a>
<ul class="sectlevel3">
<li><a href="#_script_parameters">6.1.1. Script parameters</a></li>
<li><a href="#_conditional_script">6.1.2. Conditional script</a></li>
</ul>
</li>
<li><a href="#_inputs">6.2. Inputs</a>
<ul class="sectlevel3">
<li><a href="#_input_values">6.2.1. Input values</a></li>
<li><a href="#_input_files">6.2.2. Input files</a></li>
<li><a href="#_input_path">6.2.3. Input path</a></li>
<li><a href="#_combine_input_channels">6.2.4. Combine input channels</a></li>
<li><a href="#_input_repeaters">6.2.5. Input repeaters</a></li>
</ul>
</li>
<li><a href="#_outputs">6.3. Outputs</a>
<ul class="sectlevel3">
<li><a href="#_output_values">6.3.1. Output values</a></li>
<li><a href="#_output_files">6.3.2. Output files</a></li>
<li><a href="#_multiple_output_files">6.3.3. Multiple output files</a></li>
<li><a href="#_dynamic_output_file_names">6.3.4. Dynamic output file names</a></li>
<li><a href="#_composite_inputs_and_outputs">6.3.5. Composite inputs and outputs</a></li>
</ul>
</li>
<li><a href="#_when">6.4. When</a></li>
<li><a href="#_directives">6.5. Directives</a>
<ul class="sectlevel3">
<li><a href="#_exercise_21">6.5.1. Exercise</a></li>
</ul>
</li>
<li><a href="#_organise_outputs">6.6. Organise outputs</a>
<ul class="sectlevel3">
<li><a href="#_publishdir_directive">6.6.1. PublishDir directive</a></li>
<li><a href="#_manage_semantic_sub_directories">6.6.2. Manage semantic sub-directories</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_operators">7. Operators</a>
<ul class="sectlevel2">
<li><a href="#_basic_example">7.1. Basic example</a></li>
<li><a href="#_basic_operators">7.2. Basic operators</a>
<ul class="sectlevel3">
<li><a href="#_view">7.2.1. view</a></li>
<li><a href="#_map">7.2.2. map</a></li>
<li><a href="#_into">7.2.3. into</a></li>
<li><a href="#_mix">7.2.4. mix</a></li>
<li><a href="#_flatten">7.2.5. flatten</a></li>
<li><a href="#_collect">7.2.6. collect</a></li>
<li><a href="#_grouptuple">7.2.7. groupTuple</a></li>
<li><a href="#_join">7.2.8. join</a></li>
<li><a href="#_branch">7.2.9. branch</a></li>
</ul>
</li>
<li><a href="#_more_resources_3">7.3. More resources</a></li>
</ul>
</li>
<li><a href="#_groovy_basic_structures_and_idioms">8. Groovy basic structures and idioms</a>
<ul class="sectlevel2">
<li><a href="#_printing_values">8.1. Printing values</a></li>
<li><a href="#_comments">8.2. Comments</a></li>
<li><a href="#_variables">8.3. Variables</a></li>
<li><a href="#_lists">8.4. Lists</a></li>
<li><a href="#_maps">8.5. Maps</a></li>
<li><a href="#_string_interpolation">8.6. String interpolation</a></li>
<li><a href="#_multi_line_strings">8.7. Multi-line strings</a></li>
<li><a href="#_if_statement">8.8. If statement</a></li>
<li><a href="#_for_statement">8.9. For statement</a></li>
<li><a href="#_functions">8.10. Functions</a></li>
<li><a href="#_closures">8.11. Closures</a></li>
<li><a href="#_more_resources_4">8.12. More resources</a></li>
</ul>
</li>
<li><a href="#_dsl2_and_modules">9. DSL2 and modules</a>
<ul class="sectlevel2">
<li><a href="#_basic_concepts_2">9.1. Basic concepts</a></li>
<li><a href="#_process">9.2. Process</a>
<ul class="sectlevel3">
<li><a href="#_process_definition">9.2.1. Process definition</a></li>
<li><a href="#_process_composition">9.2.2. Process composition</a></li>
<li><a href="#_process_outputs">9.2.3. Process outputs</a></li>
<li><a href="#_process_named_output">9.2.4. Process named output</a></li>
<li><a href="#_process_named_stdout">9.2.5. Process named stdout</a></li>
</ul>
</li>
<li><a href="#_workflow">9.3. Workflow</a>
<ul class="sectlevel3">
<li><a href="#_workflow_definition">9.3.1. Workflow definition</a></li>
<li><a href="#_workflow_parameters">9.3.2. Workflow parameters</a></li>
<li><a href="#_workflow_inputs">9.3.3. Workflow inputs</a></li>
<li><a href="#_workflow_outputs">9.3.4. Workflow outputs</a></li>
<li><a href="#_implicit_workflow">9.3.5. Implicit workflow</a></li>
<li><a href="#_workflow_composition">9.3.6. Workflow composition</a></li>
</ul>
</li>
<li><a href="#_modules">9.4. Modules</a>
<ul class="sectlevel3">
<li><a href="#_modules_include">9.4.1. Modules include</a></li>
<li><a href="#_multiple_inclusions">9.4.2. Multiple inclusions</a></li>
<li><a href="#_module_aliases">9.4.3. Module aliases</a></li>
<li><a href="#_module_parameters">9.4.4. Module parameters</a></li>
</ul>
</li>
<li><a href="#_dsl2_migration_notes">9.5. DSL2 migration notes</a></li>
</ul>
</li>
<li><a href="#_get_started_with_nextflow_tower">10. Get started with Nextflow Tower</a>
<ul class="sectlevel2">
<li><a href="#_basic_concepts_3">10.1. Basic concepts</a></li>
<li><a href="#_usage">10.2. Usage</a>
<ul class="sectlevel3">
<li><a href="#_via_online_gui">10.2.1. Via online GUI</a></li>
<li><a href="#_via_nextflow_run_command">10.2.2. Via Nextflow run command</a></li>
<li><a href="#_api">10.2.3. API</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_nextflow_configuration">11. Nextflow configuration</a>
<ul class="sectlevel2">
<li><a href="#_configuration_file">11.1. Configuration file</a>
<ul class="sectlevel3">
<li><a href="#_config_syntax">11.1.1. Config syntax</a></li>
<li><a href="#_config_variables">11.1.2. Config variables</a></li>
<li><a href="#_config_comments">11.1.3. Config comments</a></li>
<li><a href="#_config_scopes">11.1.4. Config scopes</a></li>
<li><a href="#_config_params">11.1.5. Config params</a></li>
<li><a href="#_config_env">11.1.6. Config env</a></li>
<li><a href="#_config_process">11.1.7. Config process</a></li>
<li><a href="#_config_docker_execution">11.1.8. Config Docker execution</a></li>
<li><a href="#_config_singularity_execution">11.1.9. Config Singularity execution</a></li>
<li><a href="#_config_conda_execution">11.1.10. Config Conda execution</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_deployment_scenarios">12. Deployment scenarios</a>
<ul class="sectlevel2">
<li><a href="#_cluster_deployment">12.1. Cluster deployment</a></li>
<li><a href="#_managing_cluster_resources">12.2. Managing cluster resources</a>
<ul class="sectlevel3">
<li><a href="#_workflow_wide_resources">12.2.1. Workflow wide resources</a></li>
<li><a href="#_configure_process_by_name">12.2.2. Configure process by name</a></li>
<li><a href="#_configure_process_by_labels">12.2.3. Configure process by labels</a></li>
<li><a href="#_configure_multiple_containers">12.2.4. Configure multiple containers</a></li>
</ul>
</li>
<li><a href="#_configuration_profiles">12.3. Configuration profiles</a></li>
<li><a href="#_cloud_deployment">12.4. Cloud deployment</a></li>
<li><a href="#_volume_mounts">12.5. Volume mounts</a></li>
<li><a href="#_custom_job_definition">12.6. Custom job definition</a></li>
<li><a href="#_custom_image">12.7. Custom image</a></li>
<li><a href="#_launch_template">12.8. Launch template</a></li>
<li><a href="#_hybrid_deployments">12.9. Hybrid deployments</a></li>
</ul>
</li>
<li><a href="#_execution_cache_and_resume">13. Execution cache and resume</a>
<ul class="sectlevel2">
<li><a href="#_how_resume_works">13.1. How resume works</a></li>
<li><a href="#_work_directory">13.2. Work directory</a></li>
<li><a href="#_how_organize_in_silico_experiments">13.3. How organize in silico experiments</a></li>
<li><a href="#_execution_provenance">13.4. Execution provenance</a></li>
<li><a href="#_resume_troubleshooting">13.5. Resume troubleshooting</a></li>
</ul>
</li>
<li><a href="#_error_handling_troubleshooting">14. Error handling & troubleshooting</a>
<ul class="sectlevel2">
<li><a href="#_execution_error_debugging">14.1. Execution error debugging</a></li>
<li><a href="#_ignore_errors">14.2. Ignore errors</a></li>
<li><a href="#_automatic_error_fail_over">14.3. Automatic error fail-over</a></li>
<li><a href="#_retry_with_backoff">14.4. Retry with backoff</a></li>
<li><a href="#_dynamic_resources_allocation">14.5. Dynamic resources allocation</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</body>
</html>