Hello Nextflow Quiz

Great stuff, you've completed all of the training material in Hello Nextflow! But, did it stick?

Test yourself with the quiz below to see how many Nextflow fundamentals you can remember :think:

Part 1: Hello World

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What is the minimum requirement for a Nextflow process?

Input and output blocks

Output and script blocks

Only a script block

Input block

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What does the output block in a process do?

Creates the output files automatically

Declares what output files to expect from the process

Determines the format of the output

Publishes outputs to a directory

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What command is used to run a Nextflow workflow?

nextflow execute script.nf

nextflow run script.nf

nextflow start script.nf

nextflow launch script.nf

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What is stored in the work/ directory?

Only the final output files

Configuration files

Temporary files for each process execution

Execution metadata like .command.sh and .exitcode

Output files from processes

Container images

Submit

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What does the -resume flag do?

Restarts the entire workflow from scratch

Skips processes that already ran with the same code, settings, and inputs

Resumes only failed processes

Saves the workflow state for later

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What is the default mode for the publishDir directive?

copy

symlink

move

hardlink

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How do you pass a parameter to a Nextflow workflow from the command line?

-parameter value

--parameter value

params.parameter = value

-p parameter=value

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Which quote type is required for variable interpolation in Nextflow?

Double quotes "

Single quotes '

Backticks `

Triple quotes """

Part 2: Hello Channels

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What is a channel in Nextflow?

A file directory

A queue-based mechanism for passing data between processes

A configuration parameter

A container registry

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Which channel factory creates a simple queue channel with values?

channel.fromPath()

channel.of()

channel.from()

channel.create()

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What happens when you pass a channel with multiple values to a process?

Only the first value is processed

The process is called once for each value in the channel

All values are processed together in a single call

The workflow fails with an error

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What does the flatten() operator do?

Unpacks array contents into individual items

Removes duplicate items from a channel

Sorts channel contents alphabetically

Converts items to lowercase

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What is the purpose of the view() operator?

To visualize the workflow structure

To inspect and print channel contents for debugging

To create graphical output

To validate channel data types

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What does the splitCsv() operator do?

Creates a CSV file from channel data

Parses CSV-formatted content, reading each line into an array

Splits a channel into multiple channels

Validates CSV formatting

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Which operator transforms channel contents element-by-element?

transform()

apply()

map()

modify()

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Why do you need dynamic filenames when processing multiple inputs?

To save disk space

To improve performance

To prevent output files from overwriting each other

To make resume work correctly

Part 3: Hello Workflow

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How do you access the output of a process in Nextflow?

processName.output

processName.out

processName.result

output.processName

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What determines the execution order of processes in a workflow?

The order they are defined in the file

Alphabetical order by process name

The dependencies between processes (output → input)

The order they are called in the workflow block

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What does the collect() operator do?

Unpacks arrays into individual items

Packages many channel items into a single array element

Removes null values from a channel

Collects error messages

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When should you use the collect() operator?

Before processing items individually in parallel

Before a process that needs all results at once

To speed up channel operations

When publishing outputs

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How do you access named outputs from a process?

processName.out[outputname]

processName.out.outputname

processName.outputname

output.processName.outputname

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What is the syntax for naming a process output?

output: path "file.txt", emit: myoutput

output: path "file.txt", name: myoutput

output: path "file.txt" as myoutput

output: path "file.txt" -> myoutput

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When passing multiple inputs to a process, what must match?

The order of inputs in the workflow call must match the input block order

The data types must all be the same

The variable names must match exactly

The number of inputs must equal the number of outputs

Part 4: Hello Modules

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What is a Nextflow module?

A configuration file

A workflow definition

A standalone file containing a single process definition

A container image

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What is the recommended filename convention for modules?

module_processName.nf

processName.nf

processName.module

processName_module.nf

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Where should module files typically be stored?

In the root directory

In the lib/ directory

In the modules/ directory

In the processes/ directory

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What is the correct syntax to import a module?

import { processName } from './modules/processName.nf'

include { processName } from './modules/processName.nf'

require { processName } from './modules/processName.nf'

use { processName } from './modules/processName.nf'

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What happens to resume functionality when you convert processes to modules?

Resume stops working

Resume only works for the main workflow

Resume continues to work normally

Resume works but cache is reset

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What are key benefits of using modules?

Faster execution time

Reduced memory usage

Reuse processes in multiple workflows without duplication

Easier maintenance - improve module once, all workflows benefit

Better code organization

Automatic parallelization

Submit

Part 5: Hello Containers

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What is a container?

A directory structure for organizing code

A lightweight, standalone executable unit with application and dependencies

A Nextflow configuration file

A type of channel

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What is the difference between a container image and instance?

They are the same thing

Image is a template; instance is a running container created from the image

Image is local; instance is remote

Instance is smaller than image

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What does the -v flag do in Docker?

Enables verbose output

Sets the Docker version

Mounts a volume to share directories between host and container

Validates the container image

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Why do you need to mount volumes when using containers?

To improve performance

To reduce disk space usage

Because containers are isolated from the host filesystem by default

To enable networking

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How do you specify a container for a Nextflow process?

docker 'image_uri' directive

container 'image_uri' directive

image 'image_uri' directive

containerImage 'image_uri' directive

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How do you enable Docker in a Nextflow workflow?

Use the -with-docker flag only

Set docker.enabled = true in the config file

Docker is enabled by default

Use the --docker parameter

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What does Nextflow automatically do when using containers?

Builds the container from a Dockerfile

Pulls the image if not already local

Mounts the work directory into the container

Runs the process script inside the container

Handles cleanup after execution

Installs Docker on the system

Creates a new container image

Submit

Part 6: Hello Config

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What file does Nextflow automatically load for configuration?

config.nf

workflow.config

nextflow.config

settings.config

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What is the configuration precedence in Nextflow?

Config file overrides CLI arguments

CLI arguments override config file values

Default values override everything

Profile settings always take precedence

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Can you enable both Docker and Conda in the same configuration?

No, only one can be enabled at a time

Yes, both can be enabled simultaneously

Only if using different profiles

Only on certain operating systems

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What happens when both Docker and Conda are enabled for a process that has both directives?

Conda is prioritized

Docker is prioritized

The workflow fails with an error

The first one defined is used

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What is the default memory allocation for a Nextflow process?

1.GB

2.GB

4.GB

It depends on the system

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How do you set resources for a specific process in the config?

process { withName: 'processName' { cpus = 4 } }

process.processName.cpus = 4

processName { cpus = 4 }

resources.processName.cpus = 4

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What command generates a resource profiling report?

nextflow run script.nf -profile

nextflow run script.nf -report

nextflow run script.nf -with-report filename.html

nextflow run script.nf --resource-report

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What is the purpose of resourceLimits in the configuration?

To set minimum resource requirements

To cap the maximum resources that can be requested

To automatically allocate optimal resources

To track resource usage over time

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What is the default executor in Nextflow?

slurm

local

cloud

batch

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How do you use a parameter file with Nextflow?

nextflow run script.nf -config file.json

nextflow run script.nf -params-file file.json

nextflow run script.nf --parameters file.json

Parameter files are loaded automatically

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What can profiles be used for in Nextflow?

User account settings

Grouping infrastructure settings (executor, container technology)

Setting different resource limits for different environments

Providing test parameter values

Performance benchmarking

Container registry authentication

Submit

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How do you use multiple profiles simultaneously?

You can only use one profile at a time

nextflow run script.nf -profile profile1 -profile profile2

nextflow run script.nf -profile profile1,profile2

Profiles are automatically merged

General Concepts

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Which of these is part of the Nextflow language?

Process

Rule

Workflow

Module

Switch

Channel

Include

Submit

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What does DSL2 refer to?

Docker Specification Language version 2

Domain-Specific Language version 2

Data Structure Library version 2

Distributed System Layer version 2

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What is the shebang required for Nextflow scripts?

#!/bin/bash

#!/usr/bin/env nextflow

#!/usr/bin/nextflow

No shebang is required

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What is the naming convention for process names in DSL2?

lowercase

camelCase

UPPERCASE

snake_case

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Which tool can generate container images from Conda packages?

DockerHub

Seqera Containers

BioContainers

Conda Cloud

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What type of quotes should be used for multi-line script blocks?

Single quotes '...'

Double quotes "..."

Triple quotes """..."""

Backticks `...`

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What is the file extension for Nextflow scripts?

.nextflow

.nf

.nx

.workflow

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Which files in the work directory are useful for debugging? (Select all that apply)

.command.sh - shows the actual command executed

.command.err - shows stderr output

.command.out - shows stdout output

.command.log - shows complete log

.exitcode - shows the exit status

.command.config - shows process configuration

Submit

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What happens if you use single quotes for a string that needs variable interpolation?

Nextflow automatically converts them to double quotes

The variable name appears literally; interpolation doesn't work

The workflow fails with a syntax error

The variable is interpolated anyway

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What does the nextflow clean command do?

Cleans up container images

Removes work subdirectories from past runs

Deletes configuration files

Clears the Nextflow cache