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‎command_line_tools‎

‎merge_trim/README.md‎

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---
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description: Specifications for merging and max length trimming of FASTQ file.
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---
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## Merge and Trim FASTQ sub-workflow specification - merge_trim_fastq.cwl
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### Tools used:
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- [merge_fastq](https://cmo-ci.gitbook.io/command-line-tools-cwl/merge_fastq_0.1.7/README.md)
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- [fastp](https://cmo-ci.gitbook.io/command-line-tools-cwl/fastp_0.24.0/README.md)
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### Usage
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```bash
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usage: ./merge_trim_fastq.cwl [-h] --merge_fastq_fastq1 MERGE_FASTQ_FASTQ1 --merge_fastq_fastq2 MERGE_FASTQ_FASTQ2 [--fastp_dont_eval_duplication] [--fastp_disable_trim_poly_g] [--fastp_disable_quality_filtering]
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[--fastp_disable_length_filtering] [--fastp_disable_adapter_trimming] [--fastp_unpaired2_output_file_name FASTP_UNPAIRED2_OUTPUT_FILE_NAME]
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[--fastp_unpaired1_output_file_name FASTP_UNPAIRED1_OUTPUT_FILE_NAME] [--fastp_read2_output_file_name FASTP_READ2_OUTPUT_FILE_NAME] [--fastp_read1_output_file_name FASTP_READ1_OUTPUT_FILE_NAME]
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[--fastp_max_len_read2 FASTP_MAX_LEN_READ2] [--fastp_max_len_read1 FASTP_MAX_LEN_READ1]
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[job_order]
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merge_trim_fastq
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positional arguments:
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job_order Job input json file
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options:
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-h, --help show this help message and exit
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--merge_fastq_fastq1 MERGE_FASTQ_FASTQ1
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Read 1 FASTQ Files that needs to merged, make sure to maintain the array order with Read 2 FASTQ files
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--merge_fastq_fastq2 MERGE_FASTQ_FASTQ2
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Read 2 FASTQ Files that needs to merged, make sure to maintain the array order with Read 1 FASTQ files
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--fastp_dont_eval_duplication
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Disable Evaluation of Duplication (default:True)
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--fastp_disable_trim_poly_g
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Disable Trim PolyG (default:True)
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--fastp_disable_quality_filtering
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Disable Quality Filtering (default:True)
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--fastp_disable_length_filtering
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Disable Length Trimming (default:True)
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--fastp_disable_adapter_trimming
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Disable Adapter Trimming (default:True)
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--fastp_unpaired2_output_file_name FASTP_UNPAIRED2_OUTPUT_FILE_NAME
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--fastp_unpaired1_output_file_name FASTP_UNPAIRED1_OUTPUT_FILE_NAME
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--fastp_read2_output_file_name FASTP_READ2_OUTPUT_FILE_NAME
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--fastp_read1_output_file_name FASTP_READ1_OUTPUT_FILE_NAME
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--fastp_max_len_read2 FASTP_MAX_LEN_READ2
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Max Lenght for Read 2 (default:95)
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--fastp_max_len_read1 FASTP_MAX_LEN_READ1
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Max Legth for READ 1 (default:95)
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```

‎merge_trim/example_input.yaml‎

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fastp_disable_trim_poly_g: null
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fastp_disable_adapter_trimming: null
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fastp_disable_length_filtering: null
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fastp_disable_quality_filtering: null
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fastp_dont_eval_duplication: null
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fastp_max_len_read1: null
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fastp_max_len_read2: null
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fastp_read1_output_file_name: null
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fastp_read2_output_file_name: null
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fastp_unpaired1_output_file_name: null
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fastp_unpaired2_output_file_name: null
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merge_fastq_fastq1:
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- class: File
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path: >-
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/path/to/fastq/L001.R1.fastq.gz
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- class: File
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path: >-
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/path/to/fastq/L002.R1.fastq.gz
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merge_fastq_fastq2:
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- class: File
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path: /path/to/fastq/L001.R2.fastq.gz
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- class: File
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path: /path/to/fastq/L002.R2.fastq.gz

‎merge_trim/merge_trim_fastq.cwl‎

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class: Workflow
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cwlVersion: v1.0
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id: merge_trim_fastq
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label: merge_trim_fastq
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$namespaces:
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s: 'https://schema.org/'
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sbg: 'https://www.sevenbridges.com/'
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inputs:
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- id: merge_fastq_fastq1
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type:
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type: array
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items: File
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inputBinding:
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prefix: '--fastq1'
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doc: >-
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Read 1 FASTQ Files that needs to merged, make sure to maintain the array
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order with Read 2 FASTQ files
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'sbg:x': 0
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'sbg:y': 321
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- id: merge_fastq_fastq2
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type:
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type: array
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items: File
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inputBinding:
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prefix: '--fastq2'
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doc: >-
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Read 2 FASTQ Files that needs to merged, make sure to maintain the array
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order with Read 1 FASTQ files
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'sbg:x': 0
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'sbg:y': 214
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- id: fastp_dont_eval_duplication
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type: boolean?
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doc: 'Disable Evaluation of Duplication (default:True)'
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'sbg:x': 327.28125
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'sbg:y': 214
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- id: fastp_disable_trim_poly_g
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type: boolean?
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doc: 'Disable Trim PolyG (default:True)'
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'sbg:x': 327.28125
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'sbg:y': 321
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- id: fastp_disable_quality_filtering
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type: boolean?
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doc: 'Disable Quality Filtering (default:True)'
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'sbg:x': 327.28125
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'sbg:y': 428
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- id: fastp_disable_length_filtering
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type: boolean?
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doc: 'Disable Length Trimming (default:True)'
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'sbg:x': 327.28125
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'sbg:y': 535
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- id: fastp_disable_adapter_trimming
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type: boolean?
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doc: 'Disable Adapter Trimming (default:True)'
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'sbg:x': 327.28125
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'sbg:y': 642
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- id: fastp_unpaired2_output_file_name
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type: string?
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'sbg:x': 0
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'sbg:y': 428
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- id: fastp_unpaired1_output_file_name
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type: string?
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'sbg:x': 0
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'sbg:y': 535
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- id: fastp_read2_output_file_name
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type: string?
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'sbg:x': 0
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'sbg:y': 642
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- id: fastp_read1_output_file_name
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type: string?
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'sbg:x': 0
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'sbg:y': 749
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- id: fastp_max_len_read2
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type: int?
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doc: 'Max Lenght for Read 2 (default:95)'
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'sbg:x': 0
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'sbg:y': 0
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- id: fastp_max_len_read1
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type: int?
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doc: 'Max Legth for READ 1 (default:95)'
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'sbg:x': 0
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'sbg:y': 107
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outputs:
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- id: fastp_unpaired2_output
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outputSource:
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- fastp_0_24_0/fastp_unpaired2_output
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type: File?
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'sbg:x': 1058.288818359375
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'sbg:y': 107
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- id: fastp_unpaired1_output
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outputSource:
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- fastp_0_24_0/fastp_unpaired1_output
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type: File?
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'sbg:x': 1058.288818359375
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'sbg:y': 214
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- id: fastp_read2_output
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outputSource:
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- fastp_0_24_0/fastp_read2_output
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type: File?
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'sbg:x': 1058.288818359375
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'sbg:y': 321
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- id: fastp_read1_output
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outputSource:
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- fastp_0_24_0/fastp_read1_output
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type: File
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'sbg:x': 1058.288818359375
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'sbg:y': 428
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- id: fastp_json_output
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outputSource:
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- fastp_0_24_0/fastp_json_output
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type: File
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'sbg:x': 1058.288818359375
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'sbg:y': 535
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- id: fastp_html_output
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outputSource:
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- fastp_0_24_0/fastp_html_output
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type: File
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'sbg:x': 1058.288818359375
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'sbg:y': 642
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steps:
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- id: merge_fastq_0_1_7
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in:
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- id: fastq1
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source:
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- merge_fastq_fastq1
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- id: fastq2
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source:
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- merge_fastq_fastq2
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out:
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- id: merge_fastq_1
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- id: merge_fastq_2
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run: ../command_line_tools/merge_fastq_0.1.7/merge_fastq_0.1.7.cwl
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'sbg:x': 327.28125
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'sbg:y': 100
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- id: fastp_0_24_0
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in:
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- id: read1_input
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source: merge_fastq_0_1_7/merge_fastq_1
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- id: read1_output_path
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default: trimmed_R1.fastq.gz
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source: fastp_read1_output_file_name
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- id: read2_input
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source: merge_fastq_0_1_7/merge_fastq_2
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- id: read2_output_path
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default: trimmed_R2.fastq.gz
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source: fastp_read2_output_file_name
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- id: unpaired1_path
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default: unpaired_R1.fastq.gz
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source: fastp_unpaired1_output_file_name
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- id: unpaired2_path
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default: unpaired_R2.fastq.gz
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source: fastp_unpaired2_output_file_name
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- id: max_len_read1
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default: 95
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source: fastp_max_len_read1
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- id: max_len_read2
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default: 95
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source: fastp_max_len_read2
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- id: disable_quality_filtering
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default: true
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source: fastp_disable_quality_filtering
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- id: disable_trim_poly_g
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default: true
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source: fastp_disable_trim_poly_g
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- id: disable_adapter_trimming
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default: true
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source: fastp_disable_adapter_trimming
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- id: dont_eval_duplication
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default: true
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source: fastp_dont_eval_duplication
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- id: disable_length_filtering
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default: true
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source: fastp_disable_length_filtering
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out:
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- id: fastp_json_output
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- id: fastp_html_output
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- id: fastp_read1_output
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- id: fastp_read2_output
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- id: fastp_unpaired1_output
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- id: fastp_unpaired2_output
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run: ../command_line_tools/fastp_0.24.0/fastp_0.24.0.cwl
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label: fastp_0.24.0
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'sbg:x': 583.671875
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'sbg:y': 290.5
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requirements: []
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$schemas:
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- 'http://schema.org/version/latest/schemaorg-current-http.rdf'
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's:author':
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- class: 's:Person'
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's:email': 'mailto:shahr2@mskcc.org'
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's:name': Ronak Shah
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's:citation': ''
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's:codeRepository': 'https://github.com/msk-access/cwl_subworkflows/merge_trim'
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's:contributor':
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- class: 's:Person'
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's:email': 'mailto:shahr2@mskcc.org'
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's:name': Ronak Shah
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's:dateCreated': '2025-03-24'
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's:license': 'https://spdx.org/licenses/Apache-2.0'

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