├── .editorconfig ├── .github └── workflows │ ├── README.md │ ├── pr-close-signal.yaml │ ├── pr-comment.yaml │ ├── pr-post-remove-branch.yaml │ ├── pr-preflight.yaml │ ├── pr-receive.yaml │ ├── sandpaper-main.yaml │ ├── sandpaper-version.txt │ ├── update-cache.yaml │ └── update-workflows.yaml ├── .gitignore ├── .gitpod.yml ├── AUTHORS ├── CITATION ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── config.yaml ├── episodes ├── 01-getting-started-with-nextflow.md ├── 02-workflow_parameters.md ├── 03-channels.md ├── 04-processes-part1.md ├── 05-processes-part2.md ├── 06-workflow.md ├── 07-operators.md ├── 08-reporting.md ├── 09-configuration.md ├── 10-workflow_checkpoint_caching.md ├── 11-Simple_Rna-Seq_pipeline.md ├── 12-nfcore.md ├── data │ └── environment.yml ├── fig │ ├── channel-files.png │ ├── channel-map.png │ ├── channel-process.png │ ├── channel-process_fastqc.jpg │ ├── channel-process_fqc.jpg │ ├── channel-process_fqc.png │ ├── dag.png │ ├── dataflow.png │ ├── execution_abstraction.png │ ├── executor.png │ ├── flowchart.png │ ├── nf-core.png │ ├── nf-executors.png │ ├── nfcore_config.png │ └── sarek_workflow.png └── files │ └── scripts │ ├── channels │ ├── channel_exercise_fromFilePairs_answer.nf │ ├── channel_exercise_fromList_answer.nf │ ├── channel_exercise_fromPath_answer.nf │ └── channel_exercise_val-queue_answer.nf │ ├── configuration │ ├── configuration_exercise-answer_process-selector.config │ ├── configuration_fastp.nf │ ├── configuration_process-labels.config │ ├── configuration_process-names.config │ ├── configuration_process_labels.nf │ ├── configuration_profile.config │ ├── print_message.config │ ├── print_message.nf │ ├── process-selector.nf │ ├── system_resources.config │ └── wc-params.config │ ├── introduction │ └── word_count.nf │ ├── modules │ ├── modules │ │ ├── module.nf │ │ ├── rnaseq-flow.nf │ │ └── rnaseq-tasks.nf │ ├── modules_addparams.nf │ ├── modules_aliases.nf │ ├── modules_aliases_02.nf │ ├── modules_exercise_add_module.nf │ ├── modules_exercise_add_module_answer.nf │ ├── modules_exercises_add_multiple_modules.nf │ ├── modules_exercises_add_multiple_modules_answers.nf │ ├── modules_index.nf │ ├── modules_multiple_inclusions.nf │ └── modules_parameters.nf │ ├── operators │ ├── operators_exercise_filter.nf │ ├── operators_exercise_filter_answer.nf │ ├── operators_exercise_grouptuple.nf │ ├── operators_exercise_grouptuple_answer.nf │ ├── operators_exercise_map.nf │ ├── operators_exercise_map_answer.nf │ ├── operators_exercise_parse-csv.nf │ ├── operators_exercise_parse-csv_answer.nf │ └── operators_join.nf │ ├── parameters │ ├── wc-params.json │ ├── wc-params.nf │ └── word_count.nf │ ├── process │ ├── process_01.nf │ ├── process_combine.nf │ ├── process_combine_02.nf │ ├── process_combine_03.nf │ ├── process_conditional.nf │ ├── process_directive.nf │ ├── process_escape_bash.nf │ ├── process_exercise_combine.nf │ ├── process_exercise_combine_answer.nf │ ├── process_exercise_directives.nf │ ├── process_exercise_directives_answers.nf │ ├── process_exercise_input.nf │ ├── process_exercise_input_answer.nf │ ├── process_exercise_output.nf │ ├── process_exercise_output_answer.nf │ ├── process_exercise_publishDir.nf │ ├── process_exercise_publishDir_answer.nf │ ├── process_exercise_repeat.nf │ ├── process_exercise_repeat_answer.nf │ ├── process_exercise_script_params.nf │ ├── process_exercise_script_params_answers.nf │ ├── process_exercise_simple_process.nf │ ├── process_exercise_tuple.nf │ ├── process_exercise_tuple_answer.nf │ ├── process_index.nf │ ├── process_index_kmer.nf │ ├── process_input_file.nf │ ├── process_input_file_02.nf │ ├── process_input_value.nf │ ├── process_multi_line.nf │ ├── process_output_file.nf │ ├── process_output_multiple.nf │ ├── process_output_multiple_dynamic.nf │ ├── process_output_path.nf │ ├── process_output_value.nf │ ├── process_publishDir.nf │ ├── process_publishDir_semantic.nf │ ├── process_python.nf │ ├── process_python_script.nf │ ├── process_reads.py │ ├── process_repeat.nf │ ├── process_rscript.nf │ ├── process_script.nf │ ├── process_script_params.nf │ ├── process_shell.nf │ ├── process_simple.nf │ ├── process_tuple_input.nf │ ├── process_tuple_io.nf │ ├── process_tuple_io_fastp.nf │ ├── process_when.nf │ └── salmon_index_combine.nf │ ├── rnaseq_pipeline │ ├── environment.yml │ ├── nextflow.config │ ├── script1.nf │ ├── script2.nf │ ├── script3.nf │ ├── script4.nf │ ├── script5.nf │ ├── script6.nf │ └── script7.nf │ └── workflow │ ├── workflow_01.nf │ ├── workflow_02.nf │ ├── workflow_03.nf │ ├── workflow_exercise.nf │ ├── workflow_exercise_02.nf │ └── workflow_exercise_answer.nf ├── index.md ├── instructors ├── instructor-notes.md └── learner_profiles.md ├── learners ├── discuss.md ├── reference.md └── setup.md ├── profiles └── learner-profiles.md ├── site └── README.md └── workflows-nextflow.Rproj /.editorconfig: 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