Nextflow Training

https://training.nextflow.io/latest/
Admin
Nextflow Training is a community-driven learning platform offering self-service courses for...
Tokens:299,901
Snippets:4,132
Trust Score:9.9
Update:2 months ago
Show doc for...
Tokens:
Raw
### Install and run plugin

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

Commands to install the plugin and execute a pipeline.

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

```bash
nextflow run greet.nf -ansi-log false
```

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

### Building and Installing Plugin

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

Command to build and install the plugin locally.

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

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

### Install and configure the plugin

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

Commands to install the plugin and update the configuration file for testing.

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

```text
// Configuration for plugin development exercises
plugins {
    id 'nf-schema@2.6.1'
    id 'nf-greeting@0.1.0'
}

greeting {
    prefix = '>>>'
    suffix = '<<<'
}
```

```text
// Configuration for plugin development exercises
plugins {
    id 'nf-schema@2.6.1'
    id 'nf-greeting@0.1.0'
}
```

```bash
nextflow run greet.nf -ansi-log false
```

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

### Pipeline execution output

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

Example output observed when starting the pipeline.

```text
N E X T F L O W   ~  version 26.04.4

Downloading plugin nf-schema@2.7.2
Launching `https://github.com/nf-core/demo` [cranky_curry] revision: 32893afef8 [master]
```

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

### View command output

Source: https://training.nextflow.io/latest/hello_nextflow/05_hello_containers?q=

Example output from listing the mounted directory.

```text
data               hello-config.nf      hello-modules.nf   hello-world.nf  nextflow.config  solutions         work
hello-channels.nf  hello-containers.nf  hello-workflow.nf  modules         results          test-params.json
```

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

### Compile and install plugin

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

Command to compile the plugin and install it into the local Nextflow plugins directory.

```bash
make install
```

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

### Pipeline configuration details

Source: https://training.nextflow.io/latest/hello_nf-core/02_rewrite_hello?q=

Example input values for the pipeline creation TUI.

```text
[ ] GitHub organisation: core
[ ] Workflow name: hello
[ ] A short description of your pipeline: A basic nf-core style version of Hello Nextflow
[ ] Name of the main author(s): < YOUR NAME >
```

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

### View Directory Contents

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

Example structure of the output directory after execution.

```text
custom-outdir-cli-2/
├── batch-report.txt
├── cowpy-COLLECTED-batch-output.txt
└── intermediates
    ├── Bonjour-output.txt
    ├── COLLECTED-batch-output.txt
    ├── Hello-output.txt
    ├── Hola-output.txt
    ├── UPPER-Bonjour-output.txt
    ├── UPPER-Hello-output.txt
    └── UPPER-Hola-output.txt
```

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

### View command output

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

Example output from the Nextflow execution.

```text
 N E X T F L O W   ~  version 26.04.4

Launching `main.nf` [clever_dijkstra] revision: a1b2c3d4e5

executor >  local (7)
[3a/f1c290] COWPY (7) | 7 of 7 ✔

Outputs:

  /workspaces/training/side-quests/metadata/results

  cowpy_art:
    - cowpy-bonjour.txt
    - cowpy-guten_tag.txt
    - cowpy-salut.txt
    - cowpy-hola.txt
    - cowpy-hello.txt
    - cowpy-hallo.txt
    - cowpy-ciao.txt
```

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

### Gradle build output

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

Example output showing a successful Gradle build process.

```text
Downloading https://services.gradle.org/distributions/gradle-8.14-bin.zip
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Welcome to Gradle 8.14!
...

Deprecated Gradle features were used in this build...

BUILD SUCCESSFUL in 23s
6 actionable tasks: 6 executed
```

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

### GreetingObserver implementation

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

Example of a basic TraceObserver that prints messages on flow creation and completion.

```groovy
/*
 * Copyright 2025, Seqera Labs
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package training.plugin

import groovy.transform.CompileStatic
import groovy.util.logging.Slf4j
import nextflow.Session
import nextflow.trace.TraceObserver

/**
 * Implements an observer that allows implementing custom
 * logic on nextflow execution events.
 */
@Slf4j
@CompileStatic
class GreetingObserver implements TraceObserver {    

    @Override
    void onFlowCreate(Session session) {            
        println "Pipeline is starting! 🚀"
    }

    @Override
    void onFlowComplete() {                         
        println "Pipeline complete! 👋"
    }
}
```

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

### Representing Metadata as a List

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

Example of a flat list structure used for metadata.

```groovy
[patientA, rep1, normal, R1, 001]
```

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

### Usage example from test profile

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

The command syntax provided in the test profile comments.

```text
    Use as follows:
        nextflow run nf-core/demo -profile test,<docker/singularity> --outdir <OUTDIR>
```

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

### Create dummy entrypoint file

Source: https://training.nextflow.io/latest/hello_nf-core/02_rewrite_hello?q=

Command to initialize a blank main.nf file for testing.

```bash
touch original-hello/main.nf
```

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

### 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
```

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

### Initialize the training project

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

Commands to set up the working directory from a solution template.

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

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

### Configure channel.fromFilePairs with glob patterns

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

Use glob patterns to match multiple files for processing. The first example shows a broad match, while the second shows a specific file path.

```nextflow
// Load files with channel.fromFilePairs
ch_files = channel.fromFilePairs('data/*_R{1,2}_001.fastq.gz')
```

```nextflow
// Load files with channel.fromFilePairs
ch_files = channel.fromFilePairs('data/patientA_rep1_normal_R{1,2}_001.fastq.gz')
```

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

### 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/splitting_and_grouping?q=

Change the current working directory to the tutorial folder.

```bash
cd side-quests/splitting_and_grouping
```

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

### 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

```

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

### Copying configuration files from solutions

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

Use these commands to initialize the modules and configuration files if starting the course from this section.

```bash
cp -r solutions/5-hello-containers/modules .
cp solutions/5-hello-containers/nextflow.config .
```

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

### Initialize plugin from Part 5 solution

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

Use this command to copy the necessary files from the previous part if starting from this section.

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

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

### Example paired FASTQ file paths

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

These file paths represent typical paired-end sequencing data where R1 and R2 denote forward and reverse reads.

```text
data/patientA_rep1_normal_R1_001.fastq.gz
data/patientA_rep1_normal_R2_001.fastq.gz
```

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

### Initialize plugin project from template

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

Copies the solution from the previous part to serve as a starting point for development.

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

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

### Define Process Input as Value

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

An example of a process definition using 'val' for input, which treats the input as a string and fails to stage the file.

```nextflow
process COUNT_LINES {
    debug true

    input:
    val input_file
```

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

### Initialize Project from Solution

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

Copy the project structure from a previous part to start the development process.

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

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

### Observer output example

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

Example of the console output generated by the onFilePublish observer method.

```text
...
📊 Tasks completed so far: 1
📁 Published: greeting.txt
📊 Tasks completed so far: 2
📁 Published: greeting.txt
...
📈 Final task count: 5
Pipeline complete! 👋
```

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

### Initialize Plugin Project

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

Commands to copy the previous solution and navigate to the plugin directory.

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

```bash
cd nf-greeting
```

```bash
cd nf-greeting
```

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

### Initialize blank configuration

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

Create an empty configuration file.

```bash
touch nextflow.config
```

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

### Install or upgrade nf-test

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

Use this command to install or update the nf-test tool to the latest version.

```bash
curl -fsSL https://code.askimed.com/install/nf-test | bash
```

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

### COWPY Usage Examples

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

Examples of using the cowpy command-line tool to generate ASCII art.

```bash
cowpy "Hello Nextflow"
```

```text
______________________________________________________
< Hello Nextflow >
------------------------------------------------------
    \   ^__^
      \  (oo)\_______
        (__)\       )\/
          ||----w |
          ||     ||
```

```bash
cowpy "Hello Nextflow" -c tux
```

```text
__________________
< Hello Nextflow >
------------------
  \
    \
        .--.
      |o_o |
      |:_/ |
      //   \ \
    (|     | )
    /'\_   _/`\
    \___)=(___/
```

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

### VCF Data Format Example

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

Example of VCF records showing variant and non-variant lines.

```text
20_10037292_10066351	3528	.	T	<NON_REF>	.	.	END=3528	GT:DP:GQ:MIN_DP:PL	0/0:19:54:19:0,54,810
20_10037292_10066351	3529	.	T	A,<NON_REF>	155.64	.	BaseQRankSum=-0.544;DP=21;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=75600,21;ReadPosRankSum=-1.158	GT:AD:DP:GQ:PL:SB	0/1:12,8,0:20:99:163,0,328,199,352,551:5,7,5,3
20_10037292_10066351	3530	.	A	<NON_REF>	.	.	END=3530	GT:DP:GQ:MIN_DP:PL	0/0:33:64:33:0,64,941
20_10037292_10066351	3531	.	A	<NON_REF>	.	.	END=3533	GT:DP:GQ:MIN_DP:PL	0/0:33:81:33:0,81,1215
20_10037292_10066351	3534	.	A	<NON_REF>	.	.	END=3534	GT:DP:GQ:MIN_DP:PL	0/0:33:78:33:0,78,1170
20_10037292_10066351	3535	.	A	<NON_REF>	.	.	END=3536	GT:DP:GQ:MIN_DP:PL	0/0:33:68:33:0,68,891
20_10037292_10066351	3537	.	A	<NON_REF>	.	.	END=3546	GT:DP:GQ:MIN_DP:PL	0/0:29:72:26:0,72,1080
```

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

### Nextflow Error Output

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

Example of the error message generated when a string is passed instead of a Path object.

```text
 N E X T F L O W   ~  version 26.04.4

Launching `main.nf` [friendly_goodall] revision: ae50609b20

File object class: class java.lang.String
[-        ] COUNT_LINES -
ERROR ~ Error executing process > 'COUNT_LINES'

Caused by:
  Not a valid path value: 'data/patientA_rep1_normal_R1_001.fastq.gz'



Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
```

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

### HPC Job Submission Syntax Examples

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

Examples of native job submission scripts for different HPC schedulers.

```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
```

```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
```

```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
```

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

### Initialize pipeline environment

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

Copy the solution directory and navigate into it to start the current training module.

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

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

### Pipeline help output

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

Example output showing the available parameters and options for the nf-core/demo pipeline.

```text
 N E X T F L O W   ~  version 26.04.4

Launching `https://github.com/nf-core/demo` [adoring_meucci] revision: 32893afef8 [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,-
                                        `._,._,'
  nf-core/demo 1.2.0
------------------------------------------------------
Typical pipeline command:

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

Input/output options
  --input                       [string] Path to a metadata file containing information about the samples in the experiment.
  --outdir                      [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

  --email                       [string] Email address for completion summary.
  --multiqc_title               [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference genome options
  --genome                      [string] Name of iGenomes reference.
  --fasta                       [string] Path to FASTA genome file.

Process skipping options
  --skip_trim                   [boolean] Skip trimming fastq files with seqtk

Generic options
  --multiqc_methods_description [string]          Custom MultiQC yaml file containing HTML including a methods description.
  --help                        [boolean, string] Display the help message.
  --help_full                   [boolean]         Display the full detailed help message.
  --show_hidden                 [boolean]         Display hidden parameters in the help message (only works when --help or --help_full are provided).
!! Hiding 19 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------

* The pipeline
    https://doi.org/10.5281/zenodo.12192442

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/demo/blob/master/CITATIONS.md
```

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

### Snapshot file content example

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

An example of the JSON structure found within an nf-test snapshot file representing process outputs.

```json
"0": [
    "hello-output.txt:md5,b1946ac92492d2347c6235b4d2611184"
]
```

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

### 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 modules from solutions

Source: https://training.nextflow.io/latest/hello_nextflow/05_hello_containers?q=

Use this command to initialize the required modules directory if starting the course from this section.

```bash
cp -r solutions/4-hello-modules/modules .
```

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

### Sample-level and Batch-level Metamap Examples

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

Examples of Groovy-style maps used for metadata, containing an 'id' field and additional sample or batch-specific information.

```groovy
[id: 'sample1', single_end: false, strandedness: 'forward']
```

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

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

### Example configuration file list

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

The output of the directory listing showing the standard configuration files included in an nf-core pipeline.

```text
base.config
containers_conda_lock_files_amd64.config
containers_conda_lock_files_arm64.config
containers_docker_amd64.config
containers_docker_arm64.config
containers_singularity_https_amd64.config
containers_singularity_https_arm64.config
containers_singularity_oras_amd64.config
containers_singularity_oras_arm64.config
igenomes.config
igenomes_ignored.config
modules.config
test.config
test_full.config
```

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

### 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
```

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

### Initialize Part 3 Workflow

Source: https://training.nextflow.io/latest/nf4_science/genomics/03_joint_calling

Commands to copy the solution files from Part 2 to set up the starting point for the joint calling assignment.

```bash
cp solutions/part2/genomics-2.nf genomics.nf
cp solutions/part2/nextflow.config .
cp solutions/part2/modules/* modules/
```

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

### Initialize the pipeline directory

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

Prepare the working directory by copying the solution from the previous training part.

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

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

### Example of .command.sh content

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

This is an example of the content found in a .command.sh file within a Nextflow work directory. It shows the actual command executed by a process task, illustrating how input files are handled.

```bash
cat work/a1/a1.txt > collected
```

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

### Pipeline execution output

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

Example output from a successful pipeline execution.

```text
 N E X T F L O W   ~  version 26.04.4

Launching `./main.nf` [modest_saha] revision: b9e9b3b8de

Downloading plugin nf-schema@2.7.2
Input/output options
  input                     : /workspaces/training/hello-nf-core/core-hello/assets/greetings.csv
  outdir                    : core-hello-results

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Generic options
  validate_params           : false
  trace_report_suffix       : 2025-12-27_06-16-55

Core Nextflow options
  runName                   : modest_saha
  containerEngine           : docker
  launchDir                 : /workspaces/training/hello-nf-core/core-hello
  workDir                   : /workspaces/training/hello-nf-core/core-hello/work
  projectDir                : /workspaces/training/hello-nf-core/core-hello
  userName                  : root
  profile                   : test,docker
  configFiles               : /workspaces/training/hello-nf-core/core-hello/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
executor >  local (8)
[a8/447993] CORE_HELLO:HELLO:sayHello (3)       | 3 of 3 ✔
[00/1fc59c] CORE_HELLO:HELLO:convertToUpper (3) | 3 of 3 ✔
[57/ac800d] CORE_HELLO:HELLO:FIND_CONCATENATE (test)     | 1 of 1 ✔
[b7/092f2b] CORE_HELLO:HELLO:COWPY              | 1 of 1 ✔
-[core/hello] Pipeline completed successfully-
```

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

### Create a working directory for experiments

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

Set up a new directory and an empty configuration file for isolated testing.

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

```bash
touch nextflow.config
```

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

### View command output for pipeline info

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

Example output showing the repository URL, local path, and available revisions for the nf-core/demo pipeline.

```text
project name: nf-core/demo
repository  : https://github.com/nf-core/demo
local path  : /workspaces/.nextflow/assets/.repos/nf-core/demo
main script : main.nf
description : An nf-core demo pipeline
revisions   :
  TEMPLATE
  bumper
  dev
  fix-nxfversion
  manually-merge-3_0_2
> master (default)
  nf-core-template-merge-2.13.2.dev0
  nf-core-template-merge-2.14.0
  nf-core-template-merge-2.14.1
  nf-core-template-merge-3.0.0
  nf-core-template-merge-3.0.1
  nf-core-template-merge-3.0.2
  nf-core-template-merge-3.1.0
  nf-core-template-merge-3.1.2
  nf-core-template-merge-3.2.0
  nf-core-template-merge-3.2.1
  nf-core-template-merge-3.3.1
  nf-core-template-merge-3.3.2
  nf-core-template-merge-4.0.0
  1.0.0 [t]
  1.0.1 [t]
  1.0.2 [t]
  1.1.0 [t]
> 1.2.0 [t]
```

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

### Default module configuration

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

Example of how default arguments are defined in modules.config.

```nextflow
    withName: FASTQC {
        ext.args   = '--quiet'
        publishDir = [
            path: { "${params.outdir}/fastqc/${meta.id}" },
            mode: params.publish_dir_mode,
            pattern: "*.{html,json}",
        ]
    }
```

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

### Navigate to project directory

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

Command to change the current working directory to the training project folder.

```bash
cd side-quests/essential_scripting_patterns
```

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

### Inspect modules.json

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

The modules.json file tracks installed modules and their repository metadata.

```json
{
    "name": "core/hello",
    "homePage": "https://github.com/core/hello",
    "repos": {
        "https://github.com/nf-core/modules.git": {
            "modules": {
                "nf-core": {
                    "find/concatenate": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": [
                            "modules"
                        ]
                    }
                }
            },
            "subworkflows": {
                "nf-core": {
                    "utils_nextflow_pipeline": {
                        "branch": "master",
                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                        "installed_by": [
                            "subworkflows"
                        ]
                    },
                    "utils_nfcore_pipeline": {
                        "branch": "master",
                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                        "installed_by": [
                            "subworkflows"
                        ]
                    },
                    "utils_nfschema_plugin": {
                        "branch": "master",
                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                        "installed_by": [
                            "subworkflows"
                        ]
                    }
                }
            }
        }
    }
}
```

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

### Initialize nf-test

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

Configure the current project for testing by creating the necessary configuration files and directory structure.

```bash
nf-test init
```

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

### Dynamic Script Execution

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

Example of a generated shell script for fastp processing.

```bash
#!/bin/bash -ue
fastp \
    --in1 SAMPLE_003_S3_L001_R1_001.fastq \
    --out1 sample_003_trimmed.fastq.gz \
    --json sample_003.fastp.json \
    --html sample_003.fastp.html \
    --thread 1
```

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

### Create Test File

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

Command to initialize the test file for the GreetingExtension class.

```bash
touch src/test/groovy/training/plugin/GreetingExtensionTest.groovy
```

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

### Nextflow execution output

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

Example output showing successful pipeline execution.

```text
 N E X T F L O W   ~  version 26.04.4

Launching `bad_syntax.nf` [small_morse] revision: 961938ee2b

executor >  local (3)
[f5/dd6f46] PROCESS_FILES (1) | 3 of 3 ✔
```

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

### Disable Plugin via Configuration

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

Example of disabling the plugin in the nextflow.config file.

```groovy
// Configuration for plugin development exercises
plugins {
    id 'nf-schema@2.6.1'
    id 'nf-greeting@0.1.0'
}

greeting {
    enabled = false
}
```

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

### Example .command.sh content

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

Shows the actual command executed by the pipeline, including the overridden arguments.

```bash
#!/usr/bin/env bash -e -u -o pipefail
printf "%s\n" sample1_R1.fastq.gz sample1_R2.fastq.gz | while read f;
do
    seqtk \
        trimfq \
        -b 5 \
        $f \
        | gzip --no-name > SAMPLE1_PE_$(basename $f)
done
...
```

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

### Define greetings.csv structure

Source: https://training.nextflow.io/latest/side_quests/plugin_development/01_plugin_basics?q=

The input CSV file used for the validation example.

```csv
greeting,language
Hello,English
Bonjour,French
Hola,Spanish
Ciao,Italian
Hallo,German
```

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

### Initialize pipeline creation

Source: https://training.nextflow.io/latest/hello_nf-core/02_rewrite_hello?q=

Command to launch the interactive nf-core pipeline creation tool.

```bash
nf-core pipelines create
```

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

### Create Configuration Class

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

Command to create the configuration class file.

```bash
touch nf-greeting/src/main/groovy/training/plugin/GreetingConfig.groovy
```

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

### Navigate and inspect project files

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

Commands to enter the plugin directory and list the generated file structure.

```bash
cd nf-greeting
```

```bash
tree
```

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

### Verify report file contents

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

Example content of the generated report file.

```text
There were 3 greetings in this batch.
```

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

### Example Command Script Content

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

Shows the content of a generated .command.sh file demonstrating the applied tool arguments.

```bash
#!/usr/bin/env bash
...
cat test.txt | cowpy -c kosh > cowpy-test.txt
```
Tokens:
Raw