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Undeclared "baseMem" variable raises an error #36
Description
Hi,
I'm currently testing nf-LO with nextflow version 26.04.6 build 12646.
While running with the test data, the following error occurs.
ERROR ~ No such variable: baseMem
-- Check '.nextflow.log' file for details
And, it seems it's because it tries to set "cpus" variable with "baseMem" on base.config file.
cpus = {
def baseCpu = params.minimap2_threads ? params.minimap2_threads as int * task.attempt : 1 * task.attempt
if (params.max_cpus){
baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int : baseMem
} else {
baseCpu
}
}
When I corrected all the places where written as "baseMem" into "baseCpu", the error above did not occur.
Activity
RenzoTale88 commentedon Aug 20, 2026
@Yoonsung1203 thanks for spotting that, an upcoming release in PR #37 should address this issue. I'll post here when it is released.
Andrea
Yoonsung1203 commentedon Aug 21, 2026
@RenzoTale88 Oh, I see. Thanks a lot!
RenzoTale88 commentedon Aug 24, 2026
@Yoonsung1203 can you try with v1.8.7:
And report back if you still come across issues with this?
Thanks
Andrea
Yoonsung1203 commentedon Aug 26, 2026
@RenzoTale88
Well, that issue seems solved, but another issue occurs in v1.8.7
It seems only a part of sequence was included in the chain file. (only the first chromosome of target was utilized for making chain)
Also, while checking the .nextflow.log file, only a single minimap2:minimap2 command ran on v1.8.7.
RenzoTale88 commentedon Aug 26, 2026
@Yoonsung1203 apologies, that was a clumsy mistake introduced when moving from using
filecalls toChannelcalls. This should soon be fixed in the upcoming release 1.8.8 #38RenzoTale88 commentedon Aug 26, 2026
@Yoonsung1203 can you try release 1.8.8?
Yoonsung1203 commentedon Aug 27, 2026
@RenzoTale88
Yes, now it works totally great.
Thanks for rapid response :)
RenzoTale88 commentedon Aug 27, 2026
@Yoonsung1203 thanks for the testing. Closed as fixed with #38