nf-core pipelines download fails with strict v2 syntax parser: includeConfig error

[kim-fehl]

Description of the bug

I’m currently experimenting with the newer strict Nextflow syntax and have export NXF_SYNTAX_PARSER=v2 set in my shell environment.

With this enabled, nf-core pipelines download scdownstream fails because nf-core/tools runs nextflow inspect, which appears to respect this environment variable. The pipeline config then fails to parse under the strict parser.

Workaround: unsetting NXF_SYNTAX_PARSER allows the download to proceed normally.

Command used and terminal output

$ export NXF_SYNTAX_PARSER=v2 && nf-core pipelines download scdownstream


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.1 - https://nf-co.re
    There is a new version of nf-core/tools available! (3.5.2)


WARNING  Could not find GitHub authentication token. Some API requests may fail.                                                                                                                                                                                                                                         
? Select release / branch: master  [branch]

In addition to the pipeline code, this tool can download software containers.
? Download software container images: docker
INFO     Detected Nextflow version 25.10.4                                                                                                                                                                                                                                                                               

If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
? Choose compression type: tar.gz
INFO     Saving 'nf-core/scdownstream'                                                                                                                                                                                                                                                                                   
         Pipeline revision: 'master'                                                                                                                                                                                                                                                                                     
         Use containers: 'docker'                                                                                                                                                                                                                                                                                        
         Container library: 'quay.io'                                                                                                                                                                                                                                                                                    
         Output file: 'nf-core-scdownstream_master.tar.gz'                                                                                                                                                                                                                                                               
         Include default institutional configuration: 'False'                                                                                                                                                                                                                                                            
INFO     Downloading workflow                                                                                                                                                                                                                                                                                            
INFO     Downloading workflow files from GitHub                                                                                                                                                                                                                                                                          
INFO     Fetching container names for workflow revision master using nextflow inspect. This might take a while.                                                                                                                                                                                                          
ERROR    Running 'nextflow inspect' failed with the following error                                                                                                                                                                                                                                                      
ERROR    Command 'nextflow inspect -format json -profile docker,test,test_full /home/kim/dev/nfcorehackathon/nf-core-scdownstream_master/master/main.nf' returned non-zero error code '1':                                                                                                                               
         >                                                                                                                                                                                                                                                                                                               
         Error nextflow.config:67:5: Unexpected input: 'includeConfig'                                                                                                                                                                                                                                                   
         │  67 |     includeConfig "${params.custom_config_base}/nfcore_custom.config"                                                                                                                                                                                                                                   
         ╰     |     ^                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                         
         ERROR ~ Config parsing failed

Relevant files

No response

System information

Nextflow version 25.10.4
nf-core/tools version 3.5.1
Desktop, Ubuntu 24.04

[nictru]

Thanks for bringing this up, I will look into it - does this hold you back for the hackathon or is this just something you noticed on the side?

[kim-fehl]

That's a minor thing for sure. In fact, it's strange to expect that the master version already fully complies to the strict syntax rules. I just don't know if you already have some migration roadmap; this issue could serve as a first step.