Zhihui
5 年之前
共有 3 個檔案被更改，包括 3 行新增 和 3 行删除
+ 1
- 1
defaults
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| "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", | "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", | ||||
| "disable_adapter_trimming": "0", | "disable_adapter_trimming": "0", | ||||
| "length_required": "50", | "length_required": "50", | ||||
| "length_required1": "20", | |||||
| "UMI": "0", | "UMI": "0", | ||||
| "umi_len": "0", | "umi_len": "0", | ||||
| "umi_loc": "umi_loc", | "umi_loc": "umi_loc", | ||||
| "length_required": "20", | |||||
| "qualified_quality_phred": "20", | "qualified_quality_phred": "20", | ||||
| "disable_quality_filtering": "0" | "disable_quality_filtering": "0" | ||||
| } | } |
+ 1
- 1
inputs
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| "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}", | "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}", | ||||
| "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}", | "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}", | ||||
| "{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}", | "{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}", | ||||
| "{{ project_name }}.length_required": "{{ length_required }}", | |||||
| "{{ project_name }}.UMI": "{{ UMI }}", | "{{ project_name }}.UMI": "{{ UMI }}", | ||||
| "{{ project_name }}.umi_loc": "{{ umi_loc }}", | "{{ project_name }}.umi_loc": "{{ umi_loc }}", | ||||
| "{{ project_name }}.umi_len": "{{ umi_len }}", | "{{ project_name }}.umi_len": "{{ umi_len }}", | ||||
| "{{ project_name }}.length_required": "{{ length_required }}", | "{{ project_name }}.length_required": "{{ length_required }}", | ||||
| "{{ project_name }}.length_required1": "{{ length_required1 }}", | |||||
| "{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}", | "{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}", | ||||
| "{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}" | "{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}" | ||||
| } | } |
+ 1
- 1
tasks/fastp.wdl
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| ##3.Trim | ##3.Trim | ||||
| if [ ${disable_adapter_trimming} -gt 0 ] | if [ ${disable_adapter_trimming} -gt 0 ] | ||||
| then | then | ||||
| fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required} --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html | |||||
| fastp --thread 4 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${sample_id}_R1.fastq.tmp2.gz -I ${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html | |||||
| else | else | ||||
| mv ${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz | mv ${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz | ||||
| mv ${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz | mv ${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz |
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