File read2 | File read2 | ||||
String adapter_sequence | String adapter_sequence | ||||
String adapter_sequence_r2 | String adapter_sequence_r2 | ||||
String docker | |||||
String cluster | |||||
String fastp_docker | |||||
String fastp_cluster | |||||
String umi_loc | String umi_loc | ||||
Int trim_front1 | Int trim_front1 | ||||
Int trim_tail1 | Int trim_tail1 |
import "./tasks/fastp.wdl" as fastp | import "./tasks/fastp.wdl" as fastp | ||||
workflow {{ project_name }} { | |||||
workflow {{ project_name }} { | |||||
File inputSamplesFile | File inputSamplesFile | ||||
Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) | Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) | ||||
scatter (quartet in inputSamples){ | scatter (quartet in inputSamples){ | ||||
call fastp.fastp as fastp { | call fastp.fastp as fastp { | ||||
input: | input: | ||||
sample_id=quartet[2], | sample_id=quartet[2], |