Hi @mashehu and @Kata Ferenc! Two questions: 1. I tried

time nf-test test tests/default.nf.test --updateSnapshot --profile test

on a new branch (

full-tests

) based on

dev

, using Nextflow v26.04.0 build 12031, and I'm getting loads of "undefined" and "not declared" errors about variables across the pipeline, for example:

Error subworkflows/local/mapped_inputs/main.nf:19:5: `files_in` was assigned but not declared
  │  19 |     files_in = row.path
  ╰     |     ^^^^^^^^

Error subworkflows/local/mapped_inputs/main.nf:21:9: `files` is not defined
  │  21 |     if (files.size() == 2){
  ╰     |         ^^^^^

Error workflows/cageseq.nf:18:1: Invalid include source: '/mnt/biggley/home/slava/projects/leancage_dev/cageseq/subworkflows/local/parameter_checks/main.nf'
  │  18 | include { PARAMETER_CHECKS } from '../subworkflows/local/parameter_che
  ╰     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I guess, this is because of the new, strict, Nextflow syntax? What are we doing with this? I can post the full list of these errors if needed. 2. Meanwhile, I'll create and populate the

<testname>.nf.test

files. In each of these files, shall I put the full list of parameters that we usually use in

.yaml

files, or just the ones that differ from the default in

cageseq/testdata/tests/params_yeast_nfcore_test_star_noindex_wfasta_se_full.yaml

? I guess, that's decided by how parameters are set by default in the schema and the pipeline itself, but I'm not sure which way we design these settings now?

1. I don't know. Did you try running outside of the test? 2. I think it would be best to use the ones that differ from default. I have the fix for default values in a PR that was blocked a bit. I will merged to dev as is, and open a new issue for adding the fixed @mashehu suggested for renaming parameters