/
01-qc-se.cwl
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01-qc-se.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
doc: 'RNA-seq 01 QC - reads: SE'
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
input_fastq_read1_files:
doc: Input read1 fastq files
type: File[]
default_adapters_file:
doc: Adapters file
type: File
nthreads:
doc: Number of threads.
type: int
outputs:
output_custom_adapters_read1:
outputSource: overrepresented_sequence_extract_read1/output_custom_adapters
type: File[]
output_fastqc_data_files_read1:
doc: FastQC data files for paired read 1
type: File[]
outputSource: extract_fastqc_data_read1/output_fastqc_data_file
output_count_raw_reads_read1:
outputSource: count_raw_reads_read1/output_read_count
type: File[]
output_fastqc_report_files_read1:
doc: FastQC reports in zip format for paired read 1
type: File[]
outputSource: fastqc_read1/output_qc_report_file
output_diff_counts_read1:
outputSource: compare_read_counts_read1/result
type: File[]
steps:
extract_basename_read1:
run: ../utils/basename.cwl
scatter: file_path
in:
file_path:
source: input_fastq_read1_files
valueFrom: $(self.basename)
sep:
valueFrom: '(\.fastq.gz|\.fastq)'
do_not_escape_sep:
valueFrom: ${return true}
out:
- basename
count_raw_reads_read1:
run: ../utils/count-fastq-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastq_file
- input_basename
in:
input_basename: extract_basename_read1/basename
input_fastq_file: input_fastq_read1_files
out:
- output_read_count
fastqc_read1:
run: ../qc/fastqc.cwl
scatter: input_fastq_file
in:
threads: nthreads
input_fastq_file: input_fastq_read1_files
out:
- output_qc_report_file
count_fastqc_reads_read1:
run: ../qc/count-fastqc-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file
input_basename: extract_basename_read1/basename
out:
- output_fastqc_read_count
extract_fastqc_data_read1:
run: ../qc/extract_fastqc_data.cwl
scatterMethod: dotproduct
scatter:
- input_qc_report_file
- input_basename
in:
input_basename: extract_basename_read1/basename
input_qc_report_file: fastqc_read1/output_qc_report_file
out:
- output_fastqc_data_file
overrepresented_sequence_extract_read1:
run: ../qc/overrepresented_sequence_extract.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file
input_basename: extract_basename_read1/basename
default_adapters_file: default_adapters_file
out:
- output_custom_adapters
compare_read_counts_read1:
run: ../qc/diff.cwl
scatterMethod: dotproduct
scatter:
- file1
- file2
in:
file2: count_fastqc_reads_read1/output_fastqc_read_count
file1: count_raw_reads_read1/output_read_count
out:
- result