Open apeltzer opened 1 year ago
I was able to reproduce the issue.
The error is raised around here. Not sure how it should be handled 🤔
@mirpedrol @mashehu @apeltzer : Perhaps the function check_for_input_mimetype can just return None
in that case?
Description of the bug
I have a customized internal pipeline that uses the nf-core template but uses only portions of it (as introduced with 2.5X release of tools):
My
.nf-core.yml
(only the relevant parts of it):This results in linting saying config variable is ignored:
But
nf-core lint
says:Which is true - it is neither in the schema nor in
nextflow.config
. If I remove the above linting exception, it throws a warning that the pipeline is missing--input
.Cross checking by just running
nf-core schema lint .
says "all fine":My expectation would be that the linting warning should not even be there....
Command used and terminal output
System information
tools 2.6, linux on centos 7