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rqcfilter.wdl
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rqcfilter.wdl
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version 1.0
import "shortReadsqc.wdl" as srqc
import "longReadsqc.wdl" as lrqc
workflow rqcfilter{
input {
Array[String] input_files
Array[String] input_fq1
Array[String] input_fq2
File? reference
String proj
Boolean interleaved
Boolean shortRead
}
if (shortRead) {
call srqc.ShortReadsQC{
input:
input_files = input_files,
input_fq1 = input_fq1,
input_fq2 = input_fq2,
interleaved = interleaved,
proj = proj
}
}
if (!shortRead) {
call lrqc.LongReadsQC{
input:
file = input_files[0],
proj = proj,
reference = reference,
}
}
output {
# short reads
File? filtered_final_srqc = ShortReadsQC.filtered_final
File? filtered_stats_final_srqc = ShortReadsQC.filtered_stats_final
File? filtered_stats2_final_srqc = ShortReadsQC.filtered_stats2_final
File? filtered_stats_json_srqc = ShortReadsQC.filter_stat_json
File? rqc_info_srqc = ShortReadsQC.rqc_info
# long reads
File? filtered_final_lrqc = LongReadsQC.filtered_final
File? filtered_stats_final_lrqc = LongReadsQC.filtered_stats1
File? filtered_stats2_final_lrqc = LongReadsQC.filtered_stats2
File? filtered_stats3_final_lrqc = LongReadsQC.filtered_stats3
File? rqc_info_lrqc = LongReadsQC.rqc_info
}
}