I’m currently following the training material of the “Hello nf-core” training. In part 2 I’m trying to run the pipeline with the test profile. However for some reason I keep getting an error, and I can’t figure out why.
training/hello-nf-core → nextflow run core-hello --outdir core-hello-results -profile test,docker --validate_params false
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 [ridiculous_boyd] 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: 2026-02-12_13-19-37
Core Nextflow options
runName : ridiculous_boyd
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 : test,docker
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]
I think that this should solve the error. See the link above for more details. These problems are already fixed in Nextflow dev, so should be solved in the next stable release
Ok, then I’m not sure why this isn’t working for you. Can you confirm that you’ve run export NXF_SYNTAX_PARSER=v1 and your version of Nextflow is 25.10.2 or later?
– Check ‘.nextflow.log’ file for details
The following invalid input values have been detected:
* --input (/home/rechal2026/.nextflow/assets/nf-core/demo/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): the file or directory ‘/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz’ does not exist (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): the file or directory ‘/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz’ does not exist (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): the file or directory ‘/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz’ does not exist (FastQ file for reads 1 must be provided, cannot contain spaces and must have extension ‘.fq.gz’ or ‘.fastq.gz’)
i realize that maybe the path “assets/samplesheet.csv” is not real. But then why it can work on CI, but cannot work on local?
Did you change the input to the pipeline to use that? As noted in the training lesson here, “An example samplesheet is also provided under the assets directory, although the paths in this one are not real.”
That file is just given as an example of how the samplesheet should be formatted.
