Nextflow config files not appearing in configFiles parameter summary display text

[scwatts]

Background

• the nf-core template uses nf-schema to display parameter summary at startup
• this includes a section for user-specified configuration files called 'configFiles'
• however, I have not been able to get user-specified configuration files to appear in this section

Replicate observation

The behaviour described above was noticed in the context of nf-core templates, and so I provide a method to replicate with the relevant tooling below.

Instructions to replicate (click to show)

Create new templated pipeline with nf-core tools v3.0.2

nf-core pipelines create \
  --name configfilesdebug \
  --description 'Debugging configFiles display text' \
  --author noone \
  --outdir configfiles-debug/

Create two NF configuration files

pushd configfiles-debug/

cat <<EOF > first.config
process {
  resourceLimits = [ cpus: 4, memory: 62.GB ]
}
EOF

cat <<EOF > second.config
process {
  withName: '*' {
    when = false
  }
}
EOF

Update to nf-schema v2.2.0 (behaviour also present in nf-schema v2.1.1)

sed -i "s#id '[email protected]'#id '[email protected]'#" nextflow.config

Run nextflow to replicate absent config files from the configFile entry of the nf-schema parameter summary display text (additionally and unrelated: assets/samplesheet.csv fails validation)

$ nextflow run -config first.config -config second.config main.nf \
  -ansi-log false \
  --input assets/samplesheet.csv \
  --outdir output/

N E X T F L O W  ~  version 24.10.0
Launching `main.nf` [hungry_curie] DSL2 - revision: 27efa5ae41

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/configfilesdebug 1.0.0dev
------------------------------------------------------
Input/output options
  input      : assets/samplesheet.csv
  outdir     : output/

Core Nextflow options
  runName    : hungry_curie
  launchDir  : /Users/stephen/temp/delete/configfiles-debug
  workDir    : /Users/stephen/temp/delete/configfiles-debug/work
  projectDir : /Users/stephen/temp/delete/configfiles-debug
  userName   : stephen
  profile    : standard
  configFiles:

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/configfilesdebug/blob/master/CITATIONS.md

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input (assets/samplesheet.csv): Validation of file failed:
	-> Entry 1: Error for field 'fastq_2' (/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz): FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'
	-> Entry 1: Error for field 'fastq_1' (/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz): FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'
	-> Entry 2: Error for field 'fastq_1' (/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz): FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'

 -- Check script './subworkflows/local/utils_nfcore_configfilesdebug_pipeline/../../nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see '.nextflow.log' file for more details

Gather software versions

$ nf-core --version


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

    nf-core/tools version 3.0.2 - https://nf-co.re


nf-core, version 3.0.2

$ nextflow -version

      N E X T F L O W
      version 24.10.0 build 5928
      created 27-10-2024 18:36 UTC (28-10-2024 05:36 AEDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

[scwatts]

I decide to take a closer look and the above PR should resolve