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- import "./tasks/fastp.wdl" as fastp
- import "./tasks/fastqc.wdl" as fastqc
-
- workflow {{ project_name }} {
- File read
- File idx
- File screen_ref_dir
- File fastq_screen_conf
- File gtf
- String sample_id
- String fastp_docker
- String adapter_sequence
- String adapter_sequence_r2
- String fastp_cluster
- String umi_loc
- String idx_prefix
- String pen_intronlen
- String fastqc_cluster_config
- String fastqc_docker
- String fastqscreen_docker
- String fastqscreen_cluster_config
- String hisat2_docker
- String hisat2_cluster
- String qualimapBAMqc_docker
- String qualimapBAMqc_cluster_config
- String qualimapRNAseq_docker
- String qualimapRNAseq_cluster_config
- String samtools_docker
- String samtools_cluster
- String stringtie_docker
- String stringtie_cluster
- String multiqc_cluster_config
- String multiqc_docker
- Int multiqc_disk_size
- 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
- Int pen_cansplice
- Int pen_noncansplice
- Int min_intronlen
- Int max_intronlen
- Int maxins
- Int minins
- Int fastqc_disk_size
- Int fastqscreen_disk_size
- Int qualimapBAMqc_disk_size
- Int qualimapRNAseq_disk_size
- Int insert_size
- Int minimum_length_allowed_for_the_predicted_transcripts
- Int Junctions_no_spliced_reads
- Int count_length
- Float minimum_isoform_abundance
- Float maximum_fraction_of_muliplelocationmapped_reads
- String ballgown_docker
- String ballgown_cluster
- String disk_size
- String count_docker
- String count_cluster
-
- call fastp.fastp as fastp {
- input:
- sample_id=sample_id,
- read = read,
- docker = fastp_docker,
- cluster = fastp_cluster,
- disk_size = disk_size,
- adapter_sequence = adapter_sequence,
- umi_loc = umi_loc,
- trim_front1 = trim_front1,
- trim_tail1 = trim_tail1,
- max_len1 = max_len1,
- 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 fastqc.fastqc as fastqc {
- input:
- read = fastp.Trim,
- docker = fastqc_docker,
- cluster_config = fastqc_cluster_config,
- disk_size = fastqc_disk_size
- }
-
- }
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