/
02-trim-pe.cwl
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02-trim-pe.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
doc: 'ChIP-seq 02 trimming - reads: PE'
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
input_read1_adapters_files:
doc: Input read 1 adapters files
type: File[]
input_read2_adapters_files:
doc: Input read 2 adapters files
type: File[]
input_read1_fastq_files:
doc: Input read 1 fastq files
type: File[]
input_read2_fastq_files:
doc: Input read 2 fastq files
type: File[]
nthreads:
default: 1
doc: Number of threads
type: int
quality_score:
default: -phred33
type: string
trimmomatic_java_opts:
doc: JVM arguments should be a quoted, space separated list
type: string?
trimmomatic_jar_path:
default: /usr/share/java/trimmomatic.jar
doc: Trimmomatic Java jar file
type: string
steps:
extract_basename_read1:
run: ../utils/basename.cwl
scatter: file_path
in:
file_path:
source: trimmomatic/output_read1_trimmed_file
valueFrom: $(self.basename)
sep:
valueFrom: '(\.fastq.gz|\.fastq)'
do_not_escape_sep:
valueFrom: ${return true}
out:
- basename
extract_basename_read2:
run: ../utils/basename.cwl
scatter: file_path
in:
file_path:
source: trimmomatic/output_read2_trimmed_paired_file
valueFrom: $(self.basename)
sep:
valueFrom: '(\.fastq.gz|\.fastq)'
do_not_escape_sep:
valueFrom: ${return true}
out:
- basename
concat_adapters:
run: ../utils/concat-files.cwl
scatterMethod: dotproduct
scatter:
- input_file1
- input_file2
in:
input_file1: input_read1_adapters_files
input_file2: input_read2_adapters_files
out:
- output_file
count_fastq_reads_read2:
run: ../utils/count-fastq-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastq_file
- input_basename
in:
input_basename: extract_basename_read2/basename
input_fastq_file: trimmomatic/output_read2_trimmed_paired_file
out:
- output_read_count
count_fastq_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: trimmomatic/output_read1_trimmed_file
out:
- output_read_count
trimmomatic:
run: ../trimmomatic/trimmomatic.cwl
scatterMethod: dotproduct
scatter:
- input_read1_fastq_file
- input_read2_fastq_file
- input_adapters_file
in:
phred:
valueFrom: '33'
nthreads: nthreads
minlen:
valueFrom: ${return 15}
input_read2_fastq_file: input_read2_fastq_files
leading:
valueFrom: ${return 3}
slidingwindow:
valueFrom: 4:20
illuminaclip:
valueFrom: 2:30:15
end_mode:
valueFrom: PE
java_opts: trimmomatic_java_opts
input_adapters_file: concat_adapters/output_file
trailing:
valueFrom: ${return 3}
trimmomatic_jar_path: trimmomatic_jar_path
input_read1_fastq_file: input_read1_fastq_files
out:
- output_read1_trimmed_file
- output_read2_trimmed_paired_file
outputs:
output_trimmed_read1_fastq_read_count:
doc: Trimmed read counts of paired read 1 fastq files
type: File[]
outputSource: count_fastq_reads_read1/output_read_count
output_data_fastq_read2_trimmed_files:
doc: Trimmed fastq files for paired read 2
type: File[]
outputSource: trimmomatic/output_read2_trimmed_paired_file
output_trimmed_read2_fastq_read_count:
doc: Trimmed read counts of paired read 2 fastq files
type: File[]
outputSource: count_fastq_reads_read2/output_read_count
output_data_fastq_read1_trimmed_files:
doc: Trimmed fastq files for paired read 1
type: File[]
outputSource: trimmomatic/output_read1_trimmed_file