I have a pipeline issue, and this is what seqera a...
# help
n
I have a pipeline issue, and this is what seqera ai tells me:
groovy.lang.MissingPropertyException: No such property: task for class: nextflow.script.dsl.ProcessDslV1
This originates from
modules/nf-core/samtools/stats/main.nf
(line 6), inside a container directive that references
task.ext.singularity_pull_docker_container
. Under Nextflow 25.10.4, the
task
object isn't accessible inside the
container
directive closure in the way this module expects — it's a known incompatibility with some older nf-core module patterns on newer Nextflow versions.
However, I have never heard of this incompatibility before (the modules also all contain the
task.ext.singularity_pull_docker_container
directive in their latest version). Can anyone confirm if this is actually a real issue?
My impression is rather that this is due to https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/bam_stats_samtools/main.nf not correctly specifying its input
p
I don't understand, do you get the error shown? It's very confusing with the DSL 1 reference there. I'd say it's hallucinating.
n
I also think it is hallucinating
I got the error shown, but the issue seems to be related to
bam_stats_samtools
expecting a fasta index, which is not really described in the module (mb I am just not getting it)