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- import "./tasks/fastp.wdl" as fastp
- workflow {{ project_name }} {
- File inputSamplesFile
- Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
- String fastp_docker
- String adapter_sequence
- String adapter_sequence_r2
- String fastp_cluster
- String umi_loc
- Int trim_front1
- Int trim_tail1
- Int max_len1
- Int trim_front2
- Int trim_tail2
- Int max_len2
- Int disable_adapter_trimming
- Int length_required
- Int umi_len
- Int UMI
- Int qualified_quality_phred
- Int length_required1
- Int disable_quality_filtering
-
- scatter (quartet in inputSamples){
- call fastp.fastp as fastp {
- input:
- sample_id= quartet[2],
- read1= quartet[0],
- read2= quartet[1],
- docker = fastp_docker,
- cluster = fastp_cluster,
- adapter_sequence = adapter_sequence,
- adapter_sequence_r2 = adapter_sequence_r2,
- umi_loc = umi_loc,
- trim_front1 = trim_front1,
- trim_tail1 = trim_tail1,
- max_len1 = max_len1,
- trim_front2 = trim_front2,
- trim_tail2 = trim_tail2,
- max_len2 = max_len2,
- disable_adapter_trimming = disable_adapter_trimming,
- length_required = length_required,
- umi_len = umi_len,
- UMI = UMI,
- qualified_quality_phred = qualified_quality_phred,
- length_required1 = length_required1,
- disable_quality_filtering = disable_quality_filtering
- }
- }
- }
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