Hello, after the release my full tests are failing from the same reason https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/48Q9Hyufz3RrAr/logs . I dont really understand since they were working in my local.
I am also trying to resume the task there but Platform raises and error as fasta and fai files are missing. But those are in the igenomes config so user doesnt need to define if --genome is given (very similar to many pipelines)
Maybe something about this line in report_benchmark_statistics?
def template_file = file(“{projectDir}/assets/datavzrd/{meta.id}.datavzrd.template.yaml”, checkIfExists: true)
Either projectDir not being understood in AWS (?)
or {meta.id} isn’t being properly mapped to one of the available asset template.yaml files?
Hey! We discussed this on slack here: Slack
It seems that two things were going on in parallel:
Platform raises and error as fasta and fai files are missing:
The JSON schema of the pipeline set fasta and fai to be required parameters, which prevented submission from platform.
AWS tests are failing:
The error is `Error: Failed to read dataset from path /nf-core-awsmegatests/work/variantbenchmarking/work-8b21c01749c4447b285d242a198127736f3ffe51/34/9e05e2990616c11bd3931715a71703/rtgtools.summary.csv`. we traced this back to the file being passed in as a String in the meta map:
[[vartype:small, id:rtgtools, csv:/omics/groups/OE0608/internal/kubran/variantbenchmarking-2/work/dd/fea9149b02bd560dfc28d37d29d71c/rtgtools.summary.csv], /omics/groups/OE0608/internal/kubran/variantbenchmarking-2/work/bd/aec7eca47f8cbed73cbe30de448220/rtgtools.datavzrd.yaml, /omics/groups/OE0608/internal/kubran/variantbenchmarking-2/assets/datavzrd/rtgtools.datavzrd.template.yaml]
This works fine locally, but on AWS this results in the file not being staged in properly. Can you try changing this to be a path and see if that works as expected?