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rtg in vcfstat

master
LUYAO REN pirms 5 gadiem
vecāks
revīzija
7c443f9f23
2 mainītis faili ar 33 papildinājumiem un 1 dzēšanām
  1. +29
    -0
      tasks/jaccard_index.wdl
  2. +4
    -1
      workflow.wdl

+ 29
- 0
tasks/jaccard_index.wdl Parādīt failu

task JI {
File vcf_a
File vcf_b
File dir_name
File sdf
String docker
String cluster_config
String disk_size
command <<<
touch number
cat ${filelist}| while read a b c d
do
rtg vcfeval -b $a -c $b -o $c -t ${sdf}
cat $c/summary.txt | sed -n '4,4p' | sed 's/\s\+/\t/g'| cut -f4-6 >> number
done
paste ${filelist} number > result.txt
>>>

runtime {
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File summary = "result.txt"
}
}

+ 4
- 1
workflow.wdl Parādīt failu

import "./tasks/multiqc.wdl" as multiqc import "./tasks/multiqc.wdl" as multiqc
import "./tasks/vcfstat.wdl" as vcfstat import "./tasks/vcfstat.wdl" as vcfstat
import "./tasks/mergeNum.wdl" as mergeNum import "./tasks/mergeNum.wdl" as mergeNum
#import "./tasks/jaccard_index.wdl" as JI




workflow {{ project_name }} { workflow {{ project_name }} {


File inputSamplesFile File inputSamplesFile
Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
# File inputJIpiarsFile
# Array[Array[File]] inputJIpairs = read_tsv(inputJIpiarsFile)
File screen_ref_dir File screen_ref_dir
File fastq_screen_conf File fastq_screen_conf
File benchmarking_dir File benchmarking_dir


call vcfstat.vcfstat as vcfstat { call vcfstat.vcfstat as vcfstat {
input: input:
rtg_vcf=benchmark.rtg_vcf
rtg_vcf=benchmark.rtg_vcf,
rtg_vcf_index=benchmark.rtg_vcf_index rtg_vcf_index=benchmark.rtg_vcf_index
} }



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