diff --git a/hmftools.wdl b/hmftools.wdl index 0b4ba6d0ede70b4fecbac475fcded6fa5285f001..76620e3cc37e291d826561a13db437ae9fa13c6a 100644 --- a/hmftools.wdl +++ b/hmftools.wdl @@ -408,13 +408,16 @@ task HealthChecker { -tum_flagstat_file ~{tumorFlagstats} \ -tum_wgs_metrics_file ~{tumorMetrics} \ -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \ - -output_dir ~{outputDir} + -output_dir ~{outputDir} + test -e '~{outputDir}/~{tumorName}.HealthCheckSucceeded' && echo 'true' > '~{outputDir}/succeeded' + test -e '~{outputDir}/~{tumorName}.HealthCheckFailed' && echo 'false' > '~{outputDir}/succeeded' } - output { - File? healthCheckSucceeded = "~{outputDir}/~{tumorName}.HealthCheckSucceeded" - File? healthCheckFailed = "~{outputDir}/~{tumorName}.HealthCheckFailed" + Boolean succeeded = read_boolean("result") + File outputFile = if succeeded + then "~{outputDir}/~{tumorName}.HealthCheckSucceeded" + else "~{outputDir}/~{tumorName}.HealthCheckFailed" } runtime {