Line of code in Training > nf-core > part 2 > 1.2 fails on me

Training
1

I am running the training using the GitHub Codespace you provided ( Sign in to GitHub · GitHub ).

In [Training > nf-core > part 2 > 1.2](Part 2: Rewrite Hello for nf-core - training.nextflow.io) the line nextflow run ./core-hello -profile docker,test --outdir core-hello-results fails on me. I get the output:

nextflow run ./core-hello -profile docker,test --outdir core-hello-results
Nextflow 25.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 25.10.2

Launching `./core-hello/main.nf` [marvelous_avogadro] DSL2 - revision: b9e9b3b8de

WARN: Unrecognized config option 'process.publishDir.path'
WARN: Unrecognized config option 'process.publishDir.mode'
WARN: Unrecognized config option 'process.publishDir.saveAs'
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
Input/output options
  outdir             : core-hello-results

Generic options
  trace_report_suffix: 2026-04-17_18-36-56

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

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
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

Instead of the expected output.

I try to continue with nf-core > part 2 but run into a similar error when in section 4.4 when I run nextflow run core-hello --outdir core-hello-results -profile test,docker --validate_params false.

2

Hi Martin, I ran through that material 2 days ago in a training and everything worked. One source of error I have seen people bump into is if they didn’t activate all the options during the templated pipeline creation step. Could you redo that step and make sure you get those exactly right?

3

I did double check this before I made the first post.

I have checked again and recorded the custom setting I set during the pipeline creation step:

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image1315×749 23.9 KB

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image1232×754 19.2 KB

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image1229×712 17.3 KB

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image1236×671 17.5 KB

When I ran nextflow run ./core-hello -profile docker,test --outdir core-hello-results, I still get:

Nextflow 25.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 25.10.2

Launching `./core-hello/main.nf` [hungry_bassi] DSL2 - revision: b9e9b3b8de

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
Input/output options
  outdir             : core-hello-results

Generic options
  trace_report_suffix: 2026-04-17_20-05-51

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

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
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
4

Ah you do need to disable the parameter validation at this stage. I think we might have left that out of the command line in the instructions, can you try again with ‘–validate_params false’ added?

5

With nextflow run ./core-hello -profile docker,test --outdir core-hello-results -–validate_params false I get:

Nextflow 25.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 25.10.2

Launching `./core-hello/main.nf` [stoic_brenner] DSL2 - revision: b9e9b3b8de

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
Input/output options
  outdir             : core-hello-results

Generic options
  validate_params    : false
  trace_report_suffix: 2026-04-17_20-19-12

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

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
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
* --validate_params (false): Value is [string] but should be [boolean]

Note I think this is the error I got when I tried to continue to nf-core > part 2 section 4.4 and ran nextflow run core-hello --outdir core-hello-results -profile test,docker --validate_params false.

6

I have also tried --validate_params False, --validate_params FALSE, --validate_params=false and --validate_params F. It can’t seem to tell I mean the boolean value.

7

Hmm ‘validate_params false’ is definitely the right syntax, it works for me. Can you just check/confirm that you’re running this with the v2 syntax parser? And are you running in codespaces or your own machine?

8

I tried export NXF_SYNTAX_PARSER=v2, closing and openning a new terminal, before rerunning nextflow run ./core-hello -profile docker,test --outdir core-hello-results --validate_params false. Got the same error.

Note Getting started - training.nextflow.io does suggest running export NXF_SYNTAX_PARSER=v1, this avoids an error I ran into Part 1: Run a demo pipeline - training.nextflow.io yesterday, see Github codespace hello-nf-core import nf-schema error - Training - Seqera Community. I ran export NXF_SYNTAX_PARSER=v1 at the start of my codespace session today.

Maybe if I start a new codespace session without first running export NXF_SYNTAX_PARSER=v1 I wont run into this problem in Part 2: Rewrite Hello for nf-core - training.nextflow.io. Will try next week.

Not sure I have given the clearest of explanations here. Have a nice weekend.

9

Oh sorry I did mean syntax v1, not v2. I’m on UK time this week so my brain is already in weekend mode. You did the right thing!

10

I’ll try running everything again first thing Monday morning and see if there’s anything that jumps out at me. Sorry for the frustrating Friday issues!

11

Just trying it now. The line below seems to be working this morning after running export NXF_SYNTAX_PARSER=v1:

nextflow run ./core-hello -profile docker,test --outdir core-hello-results

I will message when I have finished Part 2: Rewrite Hello for nf-core - training.nextflow.io, if the line nextflow run core-hello --outdir core-hello-results -profile test,docker --validate_params false works the issue is closed. Thanks for the help.

12

So this was a little odd when I reached the point when I was to run nextflow run core-hello --outdir core-hello-results -profile test,docker --validate_params false I had to rerun export NXF_SYNTAX_PARSER=v1 to get the code to work.

Is there anything that could of reset NXF_SYNTAX_PARSER to = v2. Part way through running Part 2: Rewrite Hello for nf-core - training.nextflow.io I did have a break for lunch and codespace had to be restarted as a result. Maybe that reset NXF_SYNTAX_PARSER to = v2?

13

In part 3 I can into the same issue. Had a break github codespace restarted code would not run until export NXF_SYNTAX_PARSER=v1, was run.

I have run into a seperate issue see: Line of code Training > nf-core > part 3 > 3.5 fails me - Ask for help - Seqera Community.

14

Hi Martin, yes if the codespace restarts you have to re-export any environment variables you set earlier. I’ll add that to the instructions, since I realize that’s not obvious.