Hi
I attempted to run M2 based on the configuration in gatk/Somatic_SNV_Indel_Discovery_MC, the workflow runs ok until it hits the Mutect2.oncotate_m2 step with failure messages:
Couldn't resolve all inputs for Mutect2.oncotate_m2 at index None.
causedBy:
message: Input evaluation for Call Mutect2.oncotate_m2 failed.
causedBy:
message: oncotator_docker
causedBy:
message: No coercion defined from '"broadinstitute/oncotator:1.9.3.0"' of type 'String?' to 'String'.
The oncotator parameters are set:
Mutect2.is_run_oncotator: (Boolean)"True"
Mutect2.sequencing_center: (optional String?)"Broad"
Mutect2.oncotator_docker: (optional String?)"broadinstitute/oncotator:1.9.3.0"
Mutect2.default_config_file: (optional File?)"gs://fc-099b74a5-b2e1-4f8c-8720-2ab7123fe631/oncotator/tcgaMAFManualOverrides2.4.config"
Mutect2.onco_ds_tar_gz: (optional File?)"gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz"
Is there something wrong with the Mutect2.oncotator_docker: (optional String?)"broadinstitute/oncotator:1.9.3.0" parameter?