diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index ca13b24..d2a5014 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -1,10 +1,10 @@ import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/topmed-firecloud-demo/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner -import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/develop/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker +import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.4.0/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker workflow checkerWorkflow { #File referenceFasta Int expectedNumofReads - File docker_image + String docker_image File wgs_evaluation_interval_list File wgs_coverage_interval_list @@ -37,9 +37,6 @@ workflow checkerWorkflow { Int preemptible_tries Int agg_preemptible_tries - # Get the size of the standard reference files - Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") - call TopMed_aligner.PairedEndSingleSampleWorkflow as aligner { input: #docker_image = docker_image, @@ -77,7 +74,6 @@ workflow checkerWorkflow { } - Float total_size = ref_size + size(aligner.output_cram, "GB") - call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, total_size=total_size } + call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, expectedNumofReads=expectedNumofReads, docker_image=docker_image} } diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index 2b4ba05..1343d13 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -1,9 +1,9 @@ task checkerTask { File inputCRAMFile - File referenceFasta Int expectedNumofReads - File docker_image - Float total_size + String docker_image + + Float disk_size = size(inputCRAMFile, "GB") command { printf "The CRAM file is ${inputCRAMFile}" @@ -29,6 +29,6 @@ task checkerTask { runtime { docker: docker_image - disk_size = total_size + disks: "local-disk " + sub(disk_size, "\\..*", "") + " HDD" } }