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- task MIEpos2bed {
- File mie_file
- String chromo
- String sample_name
- String docker
- String cluster_config
- String disk_size
-
- command <<<
-
- cat ${mie_file} | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.allvariants.bed
-
- cat ${mie_file} | grep -v '1:1:1' | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.mie.bed
-
- >>>
-
- runtime {
- docker:docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
- output {
- File mie_bed = "${sample_name}.${chromo}.mie.bed"
- File all_bed = "${sample_name}.${chromo}.allvariants.bed"
- }
- }
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