/
xenbase-sra-to-fastq-pe.cwl
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/
xenbase-sra-to-fastq-pe.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
inputs:
sra_input_file:
type: File
illumina_adapters_file:
type: File
threads:
type: int?
outputs:
upstream_fastq:
type: File
outputSource: trimmomatic/upstream_trimmed_file
downstream_fastq:
type: File
outputSource: trimmomatic/downstream_trimmed_file
steps:
sra_to_fastq:
run: ../tools/fastq-dump.cwl
in:
sra_file: sra_input_file
split_files:
default: true
out: [fastq_file_1, fastq_file_2]
fastqc_1:
run: ../tools/fastqc.cwl
in:
fastq_file: sra_to_fastq/fastq_file_1
out: [summary_file]
fastqc_2:
run: ../tools/fastqc.cwl
in:
fastq_file: sra_to_fastq/fastq_file_2
out: [summary_file]
fastqc_results_trigger_1:
run: ../expressiontools/fastqc-results-trigger.cwl
in:
summary_file: fastqc_1/summary_file
out: [trigger]
fastqc_results_trigger_2:
run: ../expressiontools/fastqc-results-trigger.cwl
in:
summary_file: fastqc_2/summary_file
out: [trigger]
trimmomatic:
run: ../tools/trimmomatic.cwl
in:
fastq_file_upstream: sra_to_fastq/fastq_file_1
fastq_file_downstream: sra_to_fastq/fastq_file_2
adapters_file: illumina_adapters_file
trigger:
source: [fastqc_results_trigger_1/trigger, fastqc_results_trigger_2/trigger]
valueFrom: |
${
return self[0] && self[1];
}
lib_type:
default: "PE"
illuminaclip_step_param:
default: '2:30:15'
threads: threads
out: [upstream_trimmed_file, downstream_trimmed_file]