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- import "./tasks/fastp.wdl" as fastp
- import "./tasks/pathseq.wdl" as pathseq
-
- workflow {{ project_name }} {
- String sample_id
- File fastq1
- File fastq2
- String disk_size
-
- String fastp_docker
- String fastp_cluster
- String adapter_sequence
- String adapter_sequence_r2
- 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
-
- File host_image
- File host_kmer
- File microbe_dict
- File microbe_bwa_image
- File microbe_taxonomy
-
- String pathseq_docker
- String pathseq_cluster
-
- call fastp.fastp as fastp {
- input:
- read1=fastq1,
- read2=fastq2,
- sample_id=sample_id,
- docker=fastp_docker,
- cluster=fastp_cluster,
- disk_size=disk_size,
- 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
- }
-
-
- call pathseq.pathseq as pathseq {
- input:
- sample_id=sample_id,
- fastq1=fastp.Trim_R1,
- fastq2=fastp.Trim_R2,
- host_image=host_image,
- host_kmer=host_kmer,
- microbe_dict=microbe_dict,
- microbe_bwa_image=microbe_bwa_image,
- microbe_taxonomy=microbe_taxonomy,
- disk_size=disk_size,
- docker=pathseq_docker,
- cluster=pathseq_cluster
- }
-
-
-
- }
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