The error message I received once I updated to Nextflow version 22.04.0:
No such variable: ch_software_versions_yaml
-- Check script '.nextflow/assets/nf-core/sarek/main.nf' at line: 450 or see '.nextflow.log' file for more details
Seemed like ch_software_versions_yaml is not defined correctly. I copied software_versions_mqc.yaml into sarek/assets and added the following line based on nf-core/rnaseq pipeline code (which runs fine with the new Nextflow version) and commented out line 450:
ch_software_versions_yaml = file("$projectDir/assets/software_versions_mqc.yaml", checkIfExists: true)
After this I reran the test, and received this error message:
No such variable: bwa_built
-- Check script 'sarek/main.nf' at line: 484 or see '.nextflow.log' file for more details
bwa_built variable is also defined by the command file into bwa_built, similarly to ch_software_versions_yaml, maybe this type of variable definition is not supported in Nextflow 22.04.0 anymore.
If I run NXF_VER=21.10.4 nextflow run nf-core/sarek -profile test,docker the test pipeline runs fine.
The error message I received once I updated to Nextflow version 22.04.0:
Seemed like
ch_software_versions_yamlis not defined correctly. I copiedsoftware_versions_mqc.yamlinto sarek/assets and added the following line based on nf-core/rnaseq pipeline code (which runs fine with the new Nextflow version) and commented out line 450:After this I reran the test, and received this error message:
bwa_builtvariable is also defined by the commandfile into bwa_built, similarly toch_software_versions_yaml, maybe this type of variable definition is not supported in Nextflow 22.04.0 anymore.If I run
NXF_VER=21.10.4 nextflow run nf-core/sarek -profile test,dockerthe test pipeline runs fine.