State of the Workflow 2023: The Nextflow and nf-core community survey

Section 1: About you

Section 1: About you

As part of our commitment to building a diverse and inclusive community, we want to learn more about who makes up the community. This information is anonymous and is used exclusively for the purposes of CZI Diversity and Inclusion grant reporting.

Question Title

* 1. How long have you been a Nextflow user?

I'm new to Nextflow

0-1 year

1-3 years

3-6 years

6-10 years

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* 2. Which age group do you belong to?

Under 20

20-30

31-40

41-50

51-60

60+

Prefer not to say

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* 3. Which gender do you identify as?

Male

Female

Prefer not to say

Other

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* 4. Which country do you currently live in?

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* 5. Which languages can you speak or write proficiently (Select all that apply)

English

Mandarin Chinese

Spanish

Hindi

Bengali

Portuguese

Russian

Japanese

French

Korean

German

Italian

Other (if chosen, please comment)

Question Title

* 6. What is your main area of research?

Genomics

Transcriptomics

Proteomics

Metabolomics

Metagenomics

Physics / Astronomy

Geology / Geoscience

Economics

Other (please specify)

Question Title

* 7. Which of the following statements best describe the role of open-source collaboration within your research? (Select all that apply)

It is fundamental to my research

It is useful but not essential

It facilitates co-operation across numerous countries

It provides significant time savings from how I worked previously

It provides significant financial savings

It allows my organisation to work with others

I do not find it very helpful

Section 2: Your workflow experience

Question Title

* 8. How long have you been working with scientific workflows?

I'm new to this

0-1 year

1-3 years

3-6 years

6-10 years

10+ years

Question Title

* 9. Which of the following best describes your role?

Bioinformatician

Data Scientist

Research Software Engineer

Principal Investigator / Manager

HPC or System Administrator

Other (if chosen, please comment)

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* 10. Which of the following best describes your organization?

Academia

Research Institution

Government agency

Biotech startup

Pharma organization

Healthcare/Clinical/Diagnostics

Other (if chosen, please comment)

Question Title

* 11. How many people in your organization use Nextflow pipelines?

2-5

6-10

11-20

21-50

More than 50

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* 12. Which workflow technologies do you use? (Select all that apply)

Nextflow

Snakemake

Galaxy

Airflow

Cromwell / WDL

CWL

Prefect

Apache Spark

Other (if chosen, please comment)

Question Title

* 13. How do you use Nextflow personally? (Select all that apply)

I run my own analysis using Nextflow workflows

I run analysis for others using Nextflow workflows

I set up Nextflow workflows for others to use in my organization

I write/have written my own custom in-house workflows

I am involved in developing / contributing to nf-core pipelines

I build larger systems that include Nextflow as a component

Other (if chosen, please comment)

Question Title

* 14. What type of Nextflow workflows do you use most? (Select all that apply)

I don’t run Nextflow workflows myself

Custom workflows written by me

Custom workflows written by my group

nf-core workflows

Other open-source workflows

Workflows from commercial providers

Other (if chosen, please comment)

Question Title

* 15. Which type of infrastructure do you mainly use to run your pipelines? (Select all that apply)

Single computer

On-premise cluster

Private cloud (Openstack etc)

Public cloud (AWS, Google, Azure etc)

Other (if chosen, please comment)

Question Title

* 16. Which computational platforms do you use to execute workflows? (Select all that apply)

Amazon Batch

Google Batch

Google Life Sciences

Microsoft Azure Batch

Single workstation

Grid Engine cluster

LSF cluster

PBS cluster

SLURM cluster

Kubernetes cluster (including EKS, GKE, OpenShift, Rancher etc)

Other (if chosen, please comment)

Question Title

* 17. If you have plans to migrate to the cloud in the next 2 years, which cloud provider is your preference?

Amazon Web Services

Google Cloud

Microsoft Azure

Oracle

IBM

Other (if chosen, please comment)

None of the above

Section 3: Workflow features and resources

Question Title

* 18. How important are the following aspects of a workflow system to you?

	Very unimportant	Not important	Unsure	Important	Very important
Community adoption	Community adoption Very unimportant	Community adoption Not important	Community adoption Unsure	Community adoption Important	Community adoption Very important
Industry standards	Industry standards Very unimportant	Industry standards Not important	Industry standards Unsure	Industry standards Important	Industry standards Very important
Commercial support	Commercial support Very unimportant	Commercial support Not important	Commercial support Unsure	Commercial support Important	Commercial support Very important
Documentation	Documentation Very unimportant	Documentation Not important	Documentation Unsure	Documentation Important	Documentation Very important
Ease of installation	Ease of installation Very unimportant	Ease of installation Not important	Ease of installation Unsure	Ease of installation Important	Ease of installation Very important
Native support for public cloud	Native support for public cloud Very unimportant	Native support for public cloud Not important	Native support for public cloud Unsure	Native support for public cloud Important	Native support for public cloud Very important
Graphical user interface	Graphical user interface Very unimportant	Graphical user interface Not important	Graphical user interface Unsure	Graphical user interface Important	Graphical user interface Very important
Performance at scale	Performance at scale Very unimportant	Performance at scale Not important	Performance at scale Unsure	Performance at scale Important	Performance at scale Very important
Tracking pipeline and data provenance	Tracking pipeline and data provenance Very unimportant	Tracking pipeline and data provenance Not important	Tracking pipeline and data provenance Unsure	Tracking pipeline and data provenance Important	Tracking pipeline and data provenance Very important
Workflow metrics & analytics	Workflow metrics & analytics Very unimportant	Workflow metrics & analytics Not important	Workflow metrics & analytics Unsure	Workflow metrics & analytics Important	Workflow metrics & analytics Very important
Availability of community pipelines	Availability of community pipelines Very unimportant	Availability of community pipelines Not important	Availability of community pipelines Unsure	Availability of community pipelines Important	Availability of community pipelines Very important
Portability across infrastructure and platforms	Portability across infrastructure and platforms Very unimportant	Portability across infrastructure and platforms Not important	Portability across infrastructure and platforms Unsure	Portability across infrastructure and platforms Important	Portability across infrastructure and platforms Very important
Actively developed with new features	Actively developed with new features Very unimportant	Actively developed with new features Not important	Actively developed with new features Unsure	Actively developed with new features Important	Actively developed with new features Very important
Data management functionality	Data management functionality Very unimportant	Data management functionality Not important	Data management functionality Unsure	Data management functionality Important	Data management functionality Very important

Other (if chosen, please comment)

Question Title

* 19. How important do you consider the following integrations or technologies for your current or future pipelines?

	Very unimportant	Not important	Unsure	Important	Very important
Access public databases (SRA, NCBI, etc)	Access public databases (SRA, NCBI, etc) Very unimportant	Access public databases (SRA, NCBI, etc) Not important	Access public databases (SRA, NCBI, etc) Unsure	Access public databases (SRA, NCBI, etc) Important	Access public databases (SRA, NCBI, etc) Very important
Access restricted data stored in Biobanks	Access restricted data stored in Biobanks Very unimportant	Access restricted data stored in Biobanks Not important	Access restricted data stored in Biobanks Unsure	Access restricted data stored in Biobanks Important	Access restricted data stored in Biobanks Very important
Accelerate pipelines with GPU, FPGA, etc	Accelerate pipelines with GPU, FPGA, etc Very unimportant	Accelerate pipelines with GPU, FPGA, etc Not important	Accelerate pipelines with GPU, FPGA, etc Unsure	Accelerate pipelines with GPU, FPGA, etc Important	Accelerate pipelines with GPU, FPGA, etc Very important
Use of distributed computation frameworks like Apache Spark	Use of distributed computation frameworks like Apache Spark Very unimportant	Use of distributed computation frameworks like Apache Spark Not important	Use of distributed computation frameworks like Apache Spark Unsure	Use of distributed computation frameworks like Apache Spark Important	Use of distributed computation frameworks like Apache Spark Very important
Ability to integrate with event oriented systems like Apache Kafka	Ability to integrate with event oriented systems like Apache Kafka Very unimportant	Ability to integrate with event oriented systems like Apache Kafka Not important	Ability to integrate with event oriented systems like Apache Kafka Unsure	Ability to integrate with event oriented systems like Apache Kafka Important	Ability to integrate with event oriented systems like Apache Kafka Very important
Ability to write unit tests for Nextflow workflows	Ability to write unit tests for Nextflow workflows Very unimportant	Ability to write unit tests for Nextflow workflows Not important	Ability to write unit tests for Nextflow workflows Unsure	Ability to write unit tests for Nextflow workflows Important	Ability to write unit tests for Nextflow workflows Very important
Support for jobs grouping (group multiple tasks into a single job submission)	Support for jobs grouping (group multiple tasks into a single job submission) Very unimportant	Support for jobs grouping (group multiple tasks into a single job submission) Not important	Support for jobs grouping (group multiple tasks into a single job submission) Unsure	Support for jobs grouping (group multiple tasks into a single job submission) Important	Support for jobs grouping (group multiple tasks into a single job submission) Very important
Support for jobs array (submits multiple tasks as array of jobs)	Support for jobs array (submits multiple tasks as array of jobs) Very unimportant	Support for jobs array (submits multiple tasks as array of jobs) Not important	Support for jobs array (submits multiple tasks as array of jobs) Unsure	Support for jobs array (submits multiple tasks as array of jobs) Important	Support for jobs array (submits multiple tasks as array of jobs) Very important
Support for SQL and NoSQL databases	Support for SQL and NoSQL databases Very unimportant	Support for SQL and NoSQL databases Not important	Support for SQL and NoSQL databases Unsure	Support for SQL and NoSQL databases Important	Support for SQL and NoSQL databases Very important
Ability to optimize computational resources	Ability to optimize computational resources Very unimportant	Ability to optimize computational resources Not important	Ability to optimize computational resources Unsure	Ability to optimize computational resources Important	Ability to optimize computational resources Very important
Ability to deploy workflow in hybrid environment or multi-cloud	Ability to deploy workflow in hybrid environment or multi-cloud Very unimportant	Ability to deploy workflow in hybrid environment or multi-cloud Not important	Ability to deploy workflow in hybrid environment or multi-cloud Unsure	Ability to deploy workflow in hybrid environment or multi-cloud Important	Ability to deploy workflow in hybrid environment or multi-cloud Very important

Question Title

* 20. Are the following reference and training materials useful?

	Not useful	Unsure	Very useful
Nextflow reference documentation	Nextflow reference documentation Not useful	Nextflow reference documentation Unsure	Nextflow reference documentation Very useful
Nextflow implementation patterns	Nextflow implementation patterns Not useful	Nextflow implementation patterns Unsure	Nextflow implementation patterns Very useful
Seqera Nextflow tutorial (Github)	Seqera Nextflow tutorial (Github) Not useful	Seqera Nextflow tutorial (Github) Unsure	Seqera Nextflow tutorial (Github) Very useful
Nextflow Community training	Nextflow Community training Not useful	Nextflow Community training Unsure	Nextflow Community training Very useful
Seqera and Nextflow blogs	Seqera and Nextflow blogs Not useful	Seqera and Nextflow blogs Unsure	Seqera and Nextflow blogs Very useful
Nextflow & nf-core Software Carpentries Course	Nextflow & nf-core Software Carpentries Course Not useful	Nextflow & nf-core Software Carpentries Course Unsure	Nextflow & nf-core Software Carpentries Course Very useful
nf-core website	nf-core website Not useful	nf-core website Unsure	nf-core website Very useful
nf-core #bytesize seminars	nf-core #bytesize seminars Not useful	nf-core #bytesize seminars Unsure	nf-core #bytesize seminars Very useful

Question Title

* 21. Have you attended any training or workshops which include the use or development of Nextflow pipelines? (Select all that apply)

Yes, run by Seqera Labs

Yes, run by nf-core

Yes, run by my organization

Yes, run by a 3rd party

No, but I would like to

No, not interested

Other (if chosen, please comment)