### Example: Running 'cowpy' in a Docker container

Source: https://training.nextflow.io/latest/hello_nextflow/transcripts/05_hello_containers

This example demonstrates running the 'cowpy' tool, which is installed inside a Docker image. The command is executed within a temporary container that is removed upon completion.

```bash
docker run --rm cowpy cowpy
```

--------------------------------

### Install and Build Nextflow Plugin

Source: https://training.nextflow.io/latest/side_quests/plugin_development/06_configuration

Build and install the plugin locally. Navigate to the project root after installation.

```bash
make install && cd ..
```

--------------------------------

### Build and Install Nextflow Plugin

Source: https://training.nextflow.io/latest/side_quests/plugin_development/05_observers

Navigate to the plugin directory, install it using make, and return to the parent directory. This prepares the plugin for testing.

```bash
cd nf-greeting && make install && cd ..
```

--------------------------------

### Build and Install Plugin

Source: https://training.nextflow.io/latest/side_quests/plugin_development/03_custom_functions?q=

This command sequence navigates to the plugin directory, builds it, and installs it, making it available for use in Nextflow workflows.

```bash
cd nf-greeting && make install && cd ..

```

--------------------------------

### Nextflow Command Output Example

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Example output from running the 'hello-config.nf' pipeline, showing the execution status of different tasks.

```text
 N E X T F L O W   ~  version 25.10.2

Launching `hello-config.nf` [nice_escher] DSL2 - revision: d5dfdc9872

executor > local (7)
[6a/bc46a6] sayHello (2) [100%] 3 of 3 ✔
[33/67bc48] convertToUpper (3) [100%] 3 of 3 ✔
[b5/de03ba] collectGreetings [100%] 1 of 1 ✔
[98/c6b57b] cowpy              | 1 of 1 ✔
```

--------------------------------

### Example nextflow.config Block

Source: https://training.nextflow.io/latest/side_quests/plugin_development/06_configuration

This is an example of how a user would configure the greeting prefix in their `nextflow.config` file.

```groovy
greeting {
    prefix = '>>>'
}

```

--------------------------------

### Copy Solution from Part 1

Source: https://training.nextflow.io/latest/side_quests/plugin_development/02_create_project?q=

If starting from this part, copy the solution from Part 1 to use as your starting point for plugin development.

```bash
cp -r solutions/1-plugin-basics/* .
```

--------------------------------

### Install Nextflow Plugin

Source: https://training.nextflow.io/latest/side_quests/plugin_development/02_create_project

Compiles the plugin code and installs it into the local Nextflow plugin directory.

```bash
make install

```

--------------------------------

### PBS Job Configuration Example

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Example of backend-specific syntax for PBS to request resources. This includes output file handling, queue selection, number of nodes and processors per node, and memory.

```bash
#PBS -o /path/to/my/task/directory/my-task-1.log
#PBS -j oe
#PBS -q my-science-work
#PBS -l nodes=1:ppn=5
#PBS -l mem=4gb

```

--------------------------------

### Example Directory Structure Output

Source: https://training.nextflow.io/latest/nf4_science/genomics/00_orientation

This is an example output of the `tree . -L 2` command, illustrating the project's directories and files. It's used to represent directory structures throughout the course.

```text
. 
├── data
│   ├── bam
│   ├── ref
│   └── samplesheet.csv
├── genomics.nf
├── modules
│   ├── gatk_haplotypecaller.nf
│   ├── gatk_jointgenotyping.nf
│   └── samtools_index.nf
├── nextflow.config
└── solutions
    ├── part2
    └── part3

7 directories, 6 files


```

--------------------------------

### Example Workflow Output

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

This is the expected ASCII art output from the 'hello-config.nf' workflow when run with default parameters.

```text
N E X T F L O W   ~  version 25.10.2

Launching `hello-config.nf` [disturbed_einstein] DSL2 - revision: ede9037d02

executor >  local (8)
[f0/35723c] sayHello (2)       | 3 of 3 ✔
[40/3efd1a] convertToUpper (3) | 3 of 3 ✔
[17/e97d32] collectGreetings   | 1 of 1 ✔
[98/c6b57b] cowpy              | 1 of 1 ✔
```

--------------------------------

### Example Directory Structure

Source: https://training.nextflow.io/latest/nf4_science/genomics/00_orientation?q=

This is an example output of the 'tree' command, illustrating the typical directory structure for the genomics course, including data, modules, configuration files, and solutions.

```text
.
├── data
│   ├── bam
│   ├── ref
│   └── samplesheet.csv
├── genomics.nf
├── modules
│   ├── gatk_haplotypecaller.nf
│   ├── gatk_jointgenotyping.nf
│   └── samtools_index.nf
├── nextflow.config
└── solutions
    ├── part2
    └── part3

7 directories, 6 files

```

--------------------------------

### Example Docker Command Output

Source: https://training.nextflow.io/latest/side_quests/essential_scripting_patterns

An example of the `docker run` command output, showing CPU shares and memory allocation for a task. Observe how `--cpu-shares` reflects the dynamic allocation based on sample depth.

```bash
docker run -i --cpu-shares 4096 --memory 2048m -e "NXF_TASK_WORKDIR" -v /workspaces/training/side-quests/essential_scripting_patterns:/workspaces/training/side-quests/essential_scripting_patterns -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 /bin/bash -ue /workspaces/training/side-quests/essential_scripting_patterns/work/48/6db0c9e9d8aa65e4bb4936cd3bd59e/.command.sh

```

--------------------------------

### Software Versions Report Example

Source: https://training.nextflow.io/latest/hello_nf-core/04_make_module?q=

This is an example of the `hello_software_versions.yml` report generated by nf-core pipelines, showing the software versions used for different processes ('CAT_CAT' and 'COWPY') in a pipeline run.

```yaml
CAT_CAT:
  pigz: 2.8
COWPY:
  cowpy: 1.1.5

```

--------------------------------

### SGE Job Configuration Example

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Example of backend-specific syntax for SGE to request resources. This includes output file path, job notification, queue selection, and resource limits for slots and memory.

```bash
#$ -o /path/to/my/task/directory/my-task-1.log
#$ -j y
#$ -terse
#$ -notify
#$ -q my-science-work
#$ -l slots=5
#$ -l h_rss=4096M,mem_free=4096M

```

--------------------------------

### Example `nextflow.config` Block

Source: https://training.nextflow.io/latest/side_quests/plugin_development/06_configuration?q=

This is an example of a `greeting {}` configuration block in `nextflow.config` that can be used to set custom prefix and suffix values for the greeting decorator.

```groovy
greeting {
    prefix = '>>>'
}
```

--------------------------------

### Example Parameter File (YAML)

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

An example parameter file in YAML format used to specify pipeline inputs and parameters. Note the use of colons instead of equal signs.

```yaml
input: "data/greetings.csv"
batch: "yaml"
character: "stegosaurus"
```

--------------------------------

### Start HTTP Server for Test Reports

Source: https://training.nextflow.io/latest/side_quests/plugin_development/04_build_and_test

Starts a simple Python HTTP server in the specified directory to view the generated HTML test reports. Navigate to the directory first using `pushd`.

```bash
pushd build/reports/tests/test
python -m http.server

```

--------------------------------

### SLURM Job Configuration Example

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Example of backend-specific syntax for SLURM to request resources. This includes output file path, job requeuing behavior, number of CPUs, memory, and partition.

```bash
#SBATCH -o /path/to/my/task/directory/my-task-1.log
#SBATCH --no-requeue
#SBATCH -c 8
#SBATCH --mem 4096M
#SBATCH -p my-science-work

```

--------------------------------

### Example Resolved Configuration

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config?q=

An example of the output from `nextflow config`, showing parameters, enabled features like conda, memory settings for processes, and output directory configurations.

```groovy
params {
  input = 'data/greetings.csv'
  batch = 'batch'
  character = 'turkey'
}

docker {
  enabled = false
}

conda {
  enabled = true
}

process {
  memory = '1 GB'
  withName:cowpy {
      memory = '2 GB'
      cpus = 2
  }
}

outputDir = 'custom-outdir-config/'

workflow {
  output {
      mode = 'copy'
  }
}


```

--------------------------------

### Example Docker Command Output

Source: https://training.nextflow.io/latest/side_quests/essential_scripting_patterns?q=

An example of a `docker run` command output, illustrating the CPU shares allocated to a task. This output can be used to confirm that high-depth samples receive the dynamically assigned higher CPU count.

```bash
docker run -i --cpu-shares 4096 --memory 2048m -e "NXF_TASK_WORKDIR" -v /workspaces/training/side-quests/essential_scripting_patterns:/workspaces/training/side-quests/essential_scripting_patterns -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 /bin/bash -ue /workspaces/training/side-quests/essential_scripting_patterns/work/48/6db0c9e9d8aa65e4bb4936cd3bd59e/.command.sh
```

--------------------------------

### nf-test pipeline pass example

Source: https://training.nextflow.io/latest/side_quests/nf_test

Example output showing a successful nf-test run after correcting the input file path. The test passes, indicating the pipeline executed without errors.

```text
> nf-test test tests/main.nf.test

🚀 nf-test 0.9.3
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr


Test Workflow main.nf

  Test [1d4aaf12] 'Should run without failures' PASSED (1.619s)


SUCCESS: Executed 1 tests in 1.626s

```

--------------------------------

### Resolved Default Configuration Example

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

This is an example output of the `nextflow config` command, showing parameters, docker settings, conda settings, process configurations (including name-specific overrides), output directory, and workflow output mode.

```groovy
params {
  input = 'data/greetings.csv'
  batch = 'batch'
  character = 'turkey'
}

docker {
  enabled = false
}

conda {
  enabled = true
}

process {
  memory = '1 GB'
  withName:cowpy {
      memory = '2 GB'
      cpus = 2
  }
}

outputDir = 'custom-outdir-config/'

workflow {
  output {
      mode = 'copy'
  }
}

```

--------------------------------

### Copy Solution from Part 3

Source: https://training.nextflow.io/latest/side_quests/plugin_development/04_build_and_test

Copies the solution from the previous part to use as a starting point for testing.

```bash
cp -r solutions/3-custom-functions/* .

```

--------------------------------

### Example Output Structure

Source: https://training.nextflow.io/latest/side_quests/metadata?q=

Illustrates the structure of channel elements after organizing metadata into a meta map.

```text
[
  [id:sampleA, character:squirrel],
  /workspaces/training/side-quests/metadata/data/bonjour.txt
]

```

--------------------------------

### Copy Project Solution

Source: https://training.nextflow.io/latest/side_quests/plugin_development/03_custom_functions?q=

Copies the solution from Part 2 to use as a starting point for this section.

```bash
cp -r solutions/2-create-project/* .

```

--------------------------------

### Copy and navigate to core-hello pipeline

Source: https://training.nextflow.io/latest/hello_nf-core/03_use_module?q=

Use this command to set up the 'core-hello' pipeline from the Part 2 solution as a starting point for adding modules.

```bash
cp -r solutions/core-hello-part2 core-hello
cd core-hello
```

--------------------------------

### Update Nextflow Version in build.gradle

Source: https://training.nextflow.io/latest/side_quests/plugin_development/02_create_project?q=

Modify the `nextflowVersion` in the `build.gradle` file to match your installed Nextflow version for compatibility. This example shows an updated version.

```gradle
nextflowPlugin {
    nextflowVersion = '25.10.0'

    provider = 'training'

}
```

--------------------------------

### Navigate to Project Directory

Source: https://training.nextflow.io/latest/side_quests/workflows_of_workflows

Change the current directory to the project's root for the tutorial.

```bash
cd side-quests/workflows_of_workflows
```

--------------------------------

### Complete Nextflow Script Example

Source: https://training.nextflow.io/latest/nf4_science/imaging/01_basics

A minimal Nextflow script demonstrating a single process and a workflow definition. Use this as a starting point for simple pipelines.

```nextflow
#!/usr/bin/env nextflow

/*
 * Use echo to print a greeting to a file
 */
process sayHello {

    publishDir 'results', mode: 'copy'

    input:
    val greeting

    output:
    path 'output.txt'

    script:
    """
    echo '$greeting' > output.txt
    """
}

workflow {

    // emit a greeting
    sayHello(params.greeting)
}

```

--------------------------------

### Copy and Navigate to Core-Hello Directory

Source: https://training.nextflow.io/latest/hello_nf-core/05_input_validation

Sets up the pipeline directory for the current part by copying from a previous solution and changing the current directory.

```bash
cp -r solutions/core-hello-part4 core-hello
cd core-hello
```

--------------------------------

### Channel collect() Example

Source: https://training.nextflow.io/latest/side_quests/essential_scripting_patterns

Demonstrates how the channel collect() operator gathers all emissions into a single-item channel. Requires no special setup beyond defining the channel.

```nextflow
def sample_ids = ['sample_001', 'sample_002', 'sample_003']

// channel.collect() - groups multiple channel emissions into one
ch_input = channel.fromList(sample_ids)
ch_input.view { sample -> "Individual channel item: ${sample}" }
ch_collected = ch_input.collect()
ch_collected.view { list -> "channel.collect() result: ${list} (${list.size()} items grouped into 1)" }
```

--------------------------------

### Run Initial Workflow Script

Source: https://training.nextflow.io/latest/hello_nextflow/03_hello_workflow?q=

Execute the 'hello-workflow.nf' script to ensure the initial setup is correct before making modifications.

```bash
nextflow run hello-workflow.nf
```

--------------------------------

### Get Detailed Module Information

Source: https://training.nextflow.io/latest/hello_nf-core/03_use_module?q=

This command displays comprehensive documentation for a specified module, including its repository, tools, description, inputs, outputs, and installation command.

```APIDOC
## GET /modules/info

### Description
Retrieves detailed information about a specific nf-core module from the command line.

### Method
CLI Command

### Endpoint
`nf-core modules info <module_name>`

### Parameters
#### Path Parameters
- **module_name** (string) - Required - The name of the module to get information for (e.g., `cat/cat`).

### Request Example
```bash
nf-core modules info cat/cat
```

### Response
#### Success Response (CLI Output)
- **Module Information** (object) - Contains details about the module including:
  - `Repository` (string) - URL of the module's repository.
  - `Tools` (string) - The primary tool the module is for.
  - `Description` (string) - A brief description of the module's functionality.
  - `Inputs` (array of objects) - Details about module inputs, including name, description, and pattern.
  - `Outputs` (array of objects) - Details about module outputs, including name, description, and pattern.
  - `Versions` (object) - Software version information.
  - `Installation command` (string) - The command to install the module.

#### Response Example
```
╭─ Module: cat/cat  ─────────────────────────────────────────────────╮
│ 🌐 Repository: https://github.com/nf-core/modules.git              │
│ 🔧 Tools: cat                                                      │
│ 📖 Description: A module for concatenation of gzipped or           │
│ uncompressed files                                                 │
╰────────────────────────────────────────────────────────────────────╯
                  ╷                                          ╷
📥 Inputs        │Description                               │Pattern
╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━╸
input[0]         │                                          │
╶─────────────────┼──────────────────────────────────────────┼───────╴
  meta  (map)     │Groovy Map containing sample information  │
                  │e.g. [ id:'test', single_end:false ]      │
╶─────────────────┼──────────────────────────────────────────┼───────╴
  files_in  (file)│List of compressed / uncompressed files   │      * 
                  ╵                                          ╵
                      ╷                                 ╷
📥 Outputs           │Description                      │     Pattern
╺━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸
file_out             │                                 │
╶─────────────────────┼─────────────────────────────────┼────────────╴
  meta  (map)         │Groovy Map containing sample     │
                      │information                      │
╶─────────────────────┼─────────────────────────────────┼────────────╴
  ${prefix}  (file)   │Concatenated file. Will be       │ ${file_out}
                      │gzipped if file_out ends with    │
                      │".gz"                            │
╶─────────────────────┼─────────────────────────────────┼────────────╴
versions_cat         │                                 │
╶─────────────────────┼─────────────────────────────────┼────────────╴
  versions_cat (tuple)│Software version information     │
                      ╵                                 ╵

💻  Installation command: nf-core modules install cat/cat
```
```

--------------------------------

### Run Bash Interactively in a Container

Source: https://training.nextflow.io/latest/hello_nextflow/transcripts/05_hello_containers

Use the '-it' flags to start an interactive Bash terminal session inside a Docker container. This allows you to explore the container's filesystem and run installed software.

```bash
docker run -it <image_name> bash
```

--------------------------------

### Navigate to Project Directory

Source: https://training.nextflow.io/latest/side_quests/metadata

Change the current directory to the project's root for the tutorial. This ensures all relative paths are correct.

```bash
cd side-quests/metadata
```

--------------------------------

### Run a Docker Container Interactively

Source: https://training.nextflow.io/latest/nextflow_run/02_pipeline?q=

Execute this command to start a container instance and get an interactive shell prompt inside it. The --rm flag ensures the container is removed after exiting. This is useful for exploring the container's environment.

```bash
docker run --rm -it 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
```

--------------------------------

### Navigate to Project Directory

Source: https://training.nextflow.io/latest/side_quests/working_with_files?q=

Change the current directory to the location of the tutorial files. This is a prerequisite for running the workflow.

```bash
cd side-quests/working_with_files
```

--------------------------------

### Verify Docker Buildx Installation

Source: https://training.nextflow.io/latest/envsetup/03_devcontainer

Run this command to check if Docker buildx is installed and available. If it fails, you need to install the buildx extension.

```bash
docker buildx version

```

--------------------------------

### List locally installed nf-core modules

Source: https://training.nextflow.io/latest/hello_nf-core/03_use_module?q=

This command lists all modules that have been installed locally in your pipeline project. It provides details such as the module name, repository, version SHA, a message, and the date of installation.

```bash
nf-core modules list local
```

--------------------------------

### Results Directory Contents Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/02_per_sample_variant_calling?q=

Example of output files published to the results directory.

```text
results/
└── bam/
    └── reads_mother.bam.bai -> ...

```

--------------------------------

### Create Directory and Configuration File

Source: https://training.nextflow.io/latest/nextflow_run/03_config?q=

Set up a new working directory for experiments and create a blank Nextflow configuration file within it.

```bash
mkdir -p tux-run
cd tux-run
```

```bash
touch nextflow.config
```

--------------------------------

### Batch-Level Metamap Example

Source: https://training.nextflow.io/latest/hello_nf-core/03_use_module?q=

An example of a metadata map attached at the batch level, containing an ID and a date.

```groovy
[id: 'batch1', date: '25.10.01']
```

--------------------------------

### Work Directory Contents Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/02_per_sample_variant_calling?q=

Example of files generated within the Nextflow work directory after a process completes.

```text
work/2a/e695367b2f60df09cf826b07192dc3
├── reads_mother.bam -> /workspaces/training/nf4-science/genomics/data/bam/reads_mother.bam
└── reads_mother.bam.bai

```

--------------------------------

### Example Output of greet.nf Workflow

Source: https://training.nextflow.io/latest/side_quests/plugin_development/03_custom_functions

This output shows the execution of the `greet.nf` workflow, including the reversed greetings and the decorated greetings processed by the `SAY_HELLO` process. It confirms that both the `reverseGreeting` and `decorateGreeting` functions are working as expected.

```text
N E X T F L O W   ~  version 25.10.2

Launching `greet.nf` [elated_marconi] DSL2 - revision: cd8d52c97c

Pipeline is starting! 🚀
executor >  local (5)
[fe/109754] process > SAY_HELLO (5) [100%] 5 of 5 ✔
Reversed: olleH
Reversed: ruojnoB
Reversed: àloH
Reversed: oaiC
Reversed: ollaH
Decorated: *** Hello ***
Decorated: *** Bonjour ***
Decorated: *** Holà ***
Decorated: *** Ciao ***
Decorated: *** Hallo ***
Pipeline complete! 👋

```

--------------------------------

### Nextflow Workflow Output Example

Source: https://training.nextflow.io/latest/side_quests/metadata?q=

Example output from a Nextflow workflow execution, showing processed files and augmented metadata.

```text
 N E X T F L O W   ~  version 25.10.2

Launching `main.nf` [cheeky_fermat] DSL2 - revision: d096281ee4

[4e/f722fe] IDENTIFY_LANGUAGE (7) [100%] 7 of 7, cached: 7 ✔
[[id:sampleA, character:squirrel, lang:fr], /workspaces/training/side-quests/metadata/work/eb/f7148ebdd898fbe1136bec6a714acb/bonjour.txt]
[[id:sampleB, character:tux, lang:de], /workspaces/training/side-quests/metadata/work/16/71d72410952c22cd0086d9bca03680/guten_tag.txt]
[[id:sampleC, character:sheep, lang:de], /workspaces/training/side-quests/metadata/work/ea/04f5d979429e4455e14b9242fb3b45/hallo.txt]
[[id:sampleD, character:turkey, lang:en], /workspaces/training/side-quests/metadata/work/c4/b7562adddc1cc0b7d414ec45d436eb/hello.txt]
[[id:sampleF, character:moose, lang:fr], /workspaces/training/side-quests/metadata/work/5a/6c2b84bf8fadb98e28e216426be079/salut.txt]
[[id:sampleE, character:stegosaurus, lang:es], /workspaces/training/side-quests/metadata/work/af/ee7c69bcab891c40d0529305f6b9e7/hola.txt]
```

--------------------------------

### GATK HaplotypeCaller Command Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/02_per_sample_variant_calling?q=

Example command for running GATK HaplotypeCaller for variant calling on an indexed BAM file.

```bash
gatk HaplotypeCaller \
        -R /data/ref/ref.fasta \
        -I /data/bam/reads_mother.bam \
        -O reads_mother.vcf \
        -L /data/ref/intervals.bed

```

--------------------------------

### Test convertToUpper Process - Initial Setup

Source: https://training.nextflow.io/latest/side_quests/nf_test

This snippet defines the basic structure for testing the `convertToUpper` process. It includes placeholders for parameters and process inputs, and asserts that the process should succeed.

```nf-test
nextflow_process {

    name "Test Process convertToUpper"
    script "main.nf"
    process "convertToUpper"

    test("Should run without failures") {

        when {
            params {
                // define parameters here. Example:
                // outdir = "tests/results"
            }
            process {
                """
                // define inputs of the process here. Example:
                // input[0] = file("test-file.txt")
                """
            }
        }

        then {
            assert process.success
            assert snapshot(process.out).match()
        }

    }

}
```

--------------------------------

### Nextflow Workflow Output Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/02_per_sample_variant_calling?q=

Example output from a Nextflow workflow execution, showing process completion and file indexing.

```text
N E X T F L O W   ~  version 25.10.2

┃ Launching `genomics.nf` [reverent_sinoussi] DSL2 - revision: 41d43ad7fe

executor >  local (1)
[2a/e69536] SAMTOOLS_INDEX (1) | 1 of 1 ✔

```

--------------------------------

### Copy Part 2 Solution Files

Source: https://training.nextflow.io/latest/nf4_science/rnaseq/03_multi-sample

Copies the necessary files from the Part 2 solution to set up the current directory for the multi-sample implementation.

```bash
cp solutions/part2/rnaseq-2.nf rnaseq.nf
cp solutions/part2/modules/fastqc.nf modules/
cp solutions/part2/modules/trim_galore.nf modules/
cp solutions/part2/modules/hisat2_align.nf modules/
cp solutions/part2/nextflow.config .
```

--------------------------------

### Nextflow Workflow Output Example

Source: https://training.nextflow.io/latest/hello_nextflow/01_hello_world?q=

Example output from a Nextflow workflow execution, showing process completion and file paths.

```text
 N E X T F L O W   ~  version 25.10.2

Launching `hello-world.nf` [tiny_shaw] DSL2 - revision: 757723adc1

executor >  local (1)
[df/521638] process > sayHello [100%] 1 of 1 ✔

```

--------------------------------

### FastQC Command Example

Source: https://training.nextflow.io/latest/nf4_science/rnaseq/02_single-sample?q=

This is the command-line equivalent of the FastQC step. It takes a FASTQ file as input and generates quality control reports.

```bash
fastqc <reads>

```

--------------------------------

### Install nf-core Module

Source: https://training.nextflow.io/latest/hello_nf-core/03_use_module

This command installs the 'cat/cat' module from the nf-core/modules repository into your pipeline. Ensure you are in the pipeline's root directory.

```bash
nf-core modules install cat/cat
```

--------------------------------

### Run nf-core/demo Pipeline

Source: https://training.nextflow.io/latest/hello_nf-core/01_run_demo

Example command to run the nf-core/demo pipeline. This command assumes Nextflow will resolve the pipeline code from the specified repository. Ensure you replace placeholders like '<docker/singularity/.../institute>' and '<OUTDIR>' with your specific environment and desired output directory.

```bash
nextflow run nf-core/demo \
  -profile <docker/singularity/.../institute> \
  --input samplesheet.csv \
  --outdir <OUTDIR>

```

--------------------------------

### Run Workflow with Multiple Profiles

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Combine multiple profiles using a comma-separated list with the `-profile` flag. This example runs the `hello-config.nf` workflow using the `my_laptop` and `test` profiles.

```bash
nextflow run hello-config.nf -profile my_laptop,test

```

--------------------------------

### Install Plugin via Nextflow Config

Source: https://training.nextflow.io/latest/side_quests/plugin_development/summary

Users can install your published plugin by adding its ID and version to their nextflow.config file under the plugins block.

```groovy
plugins {
    id 'nf-greeting@1.0.0'
}

```

--------------------------------

### Copy Solution from Previous Part

Source: https://training.nextflow.io/latest/side_quests/plugin_development/06_configuration?q=

If starting from this part, copy the solution files from the previous part (Part 5) to the current directory. This ensures you have a working base for implementing the configuration features.

```bash
cp -r solutions/5-observers/* .
```

--------------------------------

### Create Working Directory

Source: https://training.nextflow.io/latest/hello_nextflow/06_hello_config

Creates a new directory for experiments and navigates into it. This is the first step for setting up a run-specific configuration.

```bash
mkdir -p tux-run
cd tux-run
```

--------------------------------

### Exhausted Channel Output Example

Source: https://training.nextflow.io/latest/side_quests/debugging

Example output from a Nextflow pipeline demonstrating channel exhaustion, showing successful completion but fewer processes than expected.

```text
N E X T F L O W   ~  version 25.10.2

Launching `exhausted.nf` [extravagant_gauss] DSL2 - revision: 08cff7ba2a

executor >  local (1)
[bd/f61fff] PROCESS_FILES (1) [100%] 1 of 1 ✔

```

--------------------------------

### Spin up MultiQC Container Interactively

Source: https://training.nextflow.io/latest/nf4_science/rnaseq/01_method

Starts a Docker container interactively, mounting the local data directory to /data within the container.

```bash
docker run -it -v ./data:/data community.wave.seqera.io/library/pip_multiqc:a3c26f6199d64b7c
```

--------------------------------

### VCF File Header Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/01_method

This is an example of the header section of a VCF file generated by GATK. It includes format version, definitions for ALT and FILTER fields.

```vcf
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=PASS,Description="All filters passed">
```

--------------------------------

### Check Docker Installation

Source: https://training.nextflow.io/latest/hello_nextflow/transcripts/05_hello_containers

Verify if Docker is installed and functioning correctly on your system by checking its version. This command is useful for ensuring that Docker is ready to be used for container management.

```bash
docker -v
```

--------------------------------

### Copy solution and navigate to directory

Source: https://training.nextflow.io/latest/hello_nf-core/04_make_module

Copies the solution from Part 3 and changes the current directory to the pipeline root.

```bash
cp -r solutions/core-hello-part3 core-hello
cd core-hello
```

--------------------------------

### VCF File Content Example

Source: https://training.nextflow.io/latest/nf4_science/genomics/02_per_sample_variant_calling?q=

This is an example of the content found within a VCF (Variant Call Format) file generated by a Nextflow workflow, detailing genetic variants.

```vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	reads_mother
20_10037292_10066351	3480	.	C	CT	503.03	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.95;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,18:18:54:517,54,0
20_10037292_10066351	3520	.	AT	A	609.03	.	AC=2;AF=1.00;AN=2;DP=18;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,18:18:54:623,54,0
20_10037292_10066351	3529	.	T	A	155.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.544;DP=21;ExcessHet=0.0000;FS=1.871;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.78;ReadPosRankSum=-1.158;SOR=1.034	GT:AD:DP:GQ:PL	0/1:12,8:20:99:163,0,328
```

--------------------------------

### Return to Course Working Directory

Source: https://training.nextflow.io/latest/hello_nf-core/00_orientation

Use this command to return to the 'hello-nf-core/' directory if you navigate away from it. It assumes you are within the GitHub Codespaces training environment.

```bash
cd /workspaces/training/hello-nf-core

```

--------------------------------

### Nextflow Command Output Example

Source: https://training.nextflow.io/latest/side_quests/splitting_and_grouping

This is an example of Nextflow command output showing the pipeline version, launch details, and the processed data structure after channel operations like groupTuple.

```text
N E X T F L O W   ~  version 25.10.2

Launching `main.nf` [friendly_jang] DSL2 - revision: a1bee1c55d

[[id:patientA, interval:chr1], [patientA_rep1_normal.bam, patientA_rep2_normal.bam], [patientA_rep1_tumor.bam, patientA_rep2_tumor.bam]]
[[id:patientA, interval:chr2], [patientA_rep1_normal.bam, patientA_rep2_normal.bam], [patientA_rep1_tumor.bam, patientA_rep2_tumor.bam]]
[[id:patientA, interval:chr3], [patientA_rep1_normal.bam, patientA_rep2_normal.bam], [patientA_rep1_tumor.bam, patientA_rep2_tumor.bam]]
[[id:patientB, interval:chr1], [patientB_rep1_normal.bam], [patientB_rep1_tumor.bam]]
[[id:patientB, interval:chr2], [patientB_rep1_normal.bam], [patientB_rep1_tumor.bam]]
[[id:patientB, interval:chr3], [patientB_rep1_normal.bam], [patientB_rep1_tumor.bam]]
[[id:patientC, interval:chr1], [patientC_rep1_normal.bam], [patientC_rep1_tumor.bam]]
[[id:patientC, interval:chr2], [patientC_rep1_normal.bam], [patientC_rep1_tumor.bam]]
[[id:patientC, interval:chr3], [patientC_rep1_normal.bam], [patientC_rep1_tumor.bam]]
```

--------------------------------

### nf-test verbose output example

Source: https://training.nextflow.io/latest/side_quests/nf_test

Example of nf-test output when run with the `--verbose` flag, showing detailed Nextflow execution logs, including submitted processes and their status.

```text
> nf-test test tests/main.nf.test

🚀 nf-test 0.9.3
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr


Test Workflow main.nf

  Test [693ba951] 'Should run without failures'
    > Nextflow 24.10.4 is available - Please consider updating your version to it
    > N E X T F L O W  ~  version 24.10.0
    > Launching `/workspaces/training/side-quests/nf-test/main.nf` [zen_ampere] DSL2 - revision: bbf79d5c31
    > [2b/61e453] Submitted process > sayHello (2)
    > [31/4e1606] Submitted process > sayHello (1)
    > [bb/5209ee] Submitted process > sayHello (3)
    > [83/83db6f] Submitted process > convertToUpper (2)
    > [9b/3428b1] Submitted process > convertToUpper (1)
    > [ca/0ba51b] Submitted process > convertToUpper (3)
    PASSED (5.206s)


SUCCESS: Executed 1 tests in 5.239s

```