run stuck indefinetely at sample sheet validation step using dev branch (4f212b3)

[azedinez]

Description of the bug

As per the title, a run on the dev branch with hash 4f212b3, get stuck indefinitely at input sample sheet validation. I originally had that issue with a run on Tower using AWS Batch, and I was then also able to reproduce this locally.

Command used and terminal output

nextflow run https://github.com/nf-core/rnaseq
		 -name goofy_sammet
		 -params-file https://api.tower.nf/ephemeral/rOQaPEX-orVyC_udiDntVA.json
		 -with-tower
		 -r dev

N E X T F L O W  ~  version 23.10.0
Pulling nf-core/rnaseq ...
downloaded from https://github.com/nf-core/rnaseq.git
Launching `https://github.com/nf-core/rnaseq` [goofy_sammet] DSL2 - revision: 4f212b3e90 [dev]
Downloading plugin [email protected]

Relevant files

nextflow.log.txt
GSE154058_samplesheet (1).csv

System information

Nextflow version 23.10.0
nf-core/rnaseq dev branch commit 4f212b3 (after PR #1093)
Hardware: Tower Cloud
Executor: AWS Batch
Container: Docker
OS: linux

[bounlu]

I reported the same for rnavar pipeline.

[awgymer]

Appears to be caused by this nf-validation issue

I have tested running validateParams and fromSamplesheet with the proposed fix for that issue and validation passes in < 1s.

[mirpedrol]

This should be fixed now with the new version of nf-validation 1.1.1