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- import "./tasks/fastp.wdl" as fastp
- import "./tasks/hisat2.wdl" as hisat2
- import "./tasks/samtools.wdl" as samtools
- import "./tasks/featureCounts.wdl" as featureCounts
-
-
- workflow {{ project_name }} {
- String sample_id
- File read1
- File read2
- String adapter_sequence
- String adapter_sequence_r2
- String fastp_docker
- 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
- File idx
- String idx_prefix
- String pen_intronlen
- String hisat2_docker
- String hisat2_cluster
- Int pen_cansplice
- Int pen_noncansplice
- Int min_intronlen
- Int max_intronlen
- Int maxins
- Int minins
- String ins_size = sample_id + ".ins_size"
- String samtools_docker
- String samtools_cluster
- Int insert_size
- File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
- String gtf_dir = "oss://pgx-reference-data/reference/subread/"
- String subread_docker
- String subread_cluster
- Int cpu_num = 4
- Int strand_information = 0
-
- call fastp.fastp as fastp {
- input:
- sample_id = sample_id,
- read1 = read1,
- read2 = read2,
- 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
- }
-
- call hisat2.hisat2 as hisat2 {
- input:
- sample_id = sample_id,
- idx = idx,
- idx_prefix = idx_prefix,
- Trim_R1 = fastp.Trim_R1,
- Trim_R2 = fastp.Trim_R2,
- docker = hisat2_docker,
- cluster = hisat2_cluster,
- pen_intronlen = pen_intronlen,
- pen_cansplice = pen_cansplice,
- pen_noncansplice = pen_noncansplice,
- min_intronlen = min_intronlen,
- max_intronlen = max_intronlen,
- maxins = maxins,
- minins = minins
- }
-
- call samtools.samtools as samtools {
- input:
- sample_id = sample_id,
- sam = hisat2.sam,
- docker = samtools_docker,
- cluster = samtools_cluster,
- insert_size = insert_size
- }
-
- call featureCounts.featureCounts as featureCounts {
- input:
- sample_id = sample_id,
- bam_file = samtools.out_bam,
- lnc_gtf_file = lnc_gtf_file,
- gtf_dir = gtf_dir,
- docker = subread_docker,
- cluster = subread_cluster,
- cpu_num = cpu_num,
- strand_information = strand_information
- }
- }
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