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SRA2Fastq0.0.4.wdl
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SRA2Fastq0.0.4.wdl
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#########################################
# This is a WDL File #
# This file was formed for SRA to Fastq #
# Author: Sun Hao #
# Date: YYYY/MM/DD 2024/03/06 #
#########################################
version 1.0
task SRAtoFastq {
input {
File sra_file_paths
Int ncpu = 4
Int memory_gb = 8
}
command {
fasterq-dump -vvv -x ${sra_file_paths} -O ./
}
runtime {
cpu: ncpu
memory: "~{memory_gb} GB"
disks: "local-disk 300 HDD"
docker: "registry-vpc.miracle.ac.cn/biocontainers/sra-toolkit:v2.9.3dfsg-1b1-deb_cv1"
}
output {
Array[File] fastq_files = glob("./*.fastq")
}
}
workflow ConvertSRAtoFastq {
input {
String sra_file_paths
}
call SRAtoFastq {
input:
sra_file_paths = sra_file_paths
}
output {
Array[File] fastq_files = SRAtoFastq.fastq_files
}
}