I run again with the local fastq files.

nextflow run pinellolab/CRISPR_Pipeline \

-r main \

-c config_hackathon_2026.js \

--outdir results_hackathon \

--input samplesheet.tsv

Nextflow 26.04.0 is available - Please consider updating your version to it N E X T F L O W ~ version 25.10.4 NOTE: Your local project version looks outdated - a different revision is available in the remote repository [6206bd632c] Launching

<https://github.com/pinellolab/CRISPR_Pipeline>

[soggy_yalow] DSL2 - revision: dc93403d6e [main] WARN: Unrecognized config option ‘process.publishDir.path’ WARN: Unrecognized config option ‘process.publishDir.mode’ WARN: Unrecognized config option ‘process.publishDir.saveAs’ WARN: Access to undefined parameter

validate_params

-- Initialise it to a default value eg.

params.validate_params = some_value

Sample: sample_null_null, Single-end: true, Files: [null, null] -[null] Pipeline completed with errors- ERROR ~ Cannot invoke method toLowerCase() on null object -- Check ‘.nextflow.log’ file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check ‘.nextflow.log’ file for details