Hi @benwinog,
I just created a new Codespaces environment to try this out. A lot has changed in the past week, so definitely worth destroying your old one and starting again.
TLDR: Create a new Codespace and you should be fine now.
Updating Nextflow
Now it comes with 25.10.2 by default, but if I try to run nextflow self-update then I see the same as you, which is odd:
training/hello-nf-core/test -> nextflow self-update
N E X T F L O W
version 25.10.3 build 10983
created 22-01-2026 15:34 UTC (15:34 GMT)
cite doi:10.1038/nbt.3820
http://nextflow.io
Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /usr/local/bin
training/hello-nf-core/test -> nextflow info
Version: 25.10.2 build 10555
Created: 28-11-2025 19:24 UTC (19:24 GMT)
System: Linux 6.8.0-1030-azure
Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 21.0.6+7-LTS
Encoding: UTF-8 (UTF-8)
I’m not sure why this is happening, I guess it’s something to do with the Devcontainers installation method. However, the good 'ol environment variable method does still work:
training/hello-nf-core/test -> export NXF_VER=25.10.3
training/hello-nf-core/test -> nextflow info
Version: 25.10.3 build 10983
Created: 22-01-2026 15:34 UTC (15:34 GMT)
System: Linux 6.8.0-1030-azure
Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 21.0.6+7-LTS
Encoding: UTF-8 (UTF-8)
Running nf-core/demo
I updated and published a new release of this pipeline last week, with the hope to make it compliant with the new Nextflow syntax parser. But sadly it’s still having problems. The closes I get is with the latest edge release of Nextflow:
training/hello-nf-core/test -> NXF_VER=25.12.0-edge NXF_EDGE=1 nextflow run nf-core/demo -profile docker,test --outdir demo-results
N E X T F L O W ~ version 25.12.0-edge
Launching `https://github.com/nf-core/demo` [irreverent_snyder] DSL2 - revision: 45904cb9d1 [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/demo 1.1.0
------------------------------------------------------
Input/output options
outdir : demo-results
Generic options
trace_report_suffix: 2026-02-08_00-08-30
Core Nextflow options
revision : master
runName : irreverent_snyder
containerEngine : docker
launchDir : /workspaces/training/hello-nf-core/test
workDir : /workspaces/training/hello-nf-core/test/work
projectDir : /workspaces/.nextflow/assets/nf-core/demo
userName : root
profile : docker,test
configFiles : /workspaces/.nextflow/assets/nf-core/demo/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/45904cb9d12db3d89900e6c479fe604ef71b297b/CITATIONS.md
Downloading plugin nf-amazon@3.6.0
ERROR ~ Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* Missing required parameter(s): input
I’m not sure why it’s complaining about --input with the test profile, need to look into that. But anyway, turning off the new Nextflow syntax parser does finally get us there:
training/hello-nf-core/test -> NXF_SYNTAX_PARSER=v1 NXF_VER=25.12.0-edge NXF_EDGE=1 nextflow run nf-core/demo -profile docker,test --outdir demo-res
ults
N E X T F L O W ~ version 25.12.0-edge
WARN: This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, but 'nf-core/demo' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command.
Launching `https://github.com/nf-core/demo` [dreamy_brattain] DSL2 - revision: 45904cb9d1 [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/demo 1.1.0
------------------------------------------------------
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
outdir : demo-results
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Generic options
trace_report_suffix : 2026-02-08_00-10-28
Core Nextflow options
revision : master
runName : dreamy_brattain
containerEngine : docker
launchDir : /workspaces/training/hello-nf-core/test
workDir : /workspaces/training/hello-nf-core/test/work
projectDir : /workspaces/.nextflow/assets/nf-core/demo
userName : root
profile : docker,test
configFiles : /workspaces/.nextflow/assets/nf-core/demo/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/45904cb9d12db3d89900e6c479fe604ef71b297b/CITATIONS.md
executor > local (1)
[08/94f19e] NFCORE_DEMO:DEMO:FASTQC (SAMPLE1_PE) [ 0%] 0 of 3
[- ] NFCORE_DEMO:DEMO:SEQTK_TRIM [ 0%] 0 of 3
[- ] NFCORE_DEMO:DEMO:MULTIQC -
And indeed, it also works with 25.10.2 if $NXF_SYNTAX_PARSER is set to v1 as the training stipulates at the start.
TLDR
Create a new Codespace from scratch, follow the docs - including the export NXF_SYNTAX_PARSER=v1 statement - and everything should now work.
We’re actively working on making this all smooth with the new syntax parser, so hopefully in a month or two we’ll be able to have the nf-core course run in the same modern way as all other courses.
Phil