"fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", | "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", | ||||
"fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6", | "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6", | ||||
"fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc", | "fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc", | ||||
"trim_front1": "0", | |||||
"trim_tail1": "0", | |||||
"max_len1": "0", | |||||
"trim_front2": "0", | |||||
"trim_tail2": "0", | |||||
"max_len2": "0", | |||||
"adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA", | "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA", | ||||
"adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", | "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", | ||||
"disable_adapter_trimming": "0", | |||||
"length_required": "50", | |||||
"length_required1": "20", | |||||
"umi_len": "0", | |||||
"umi_loc": "umi_loc", | |||||
"qualified_quality_phred": "20", | |||||
"hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2", | "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2", | ||||
"hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc", | "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc", | ||||
"samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1", | "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1", |
"{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}", | "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}", | ||||
"{{ project_name }}.fastp_docker": "{{ fastp_docker }}", | "{{ project_name }}.fastp_docker": "{{ fastp_docker }}", | ||||
"{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}", | "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}", | ||||
"{{ project_name }}.trim_front1": "{{ trim_front1 }}", | |||||
"{{ project_name }}.trim_tail1": "{{ trim_tail1 }}", | |||||
"{{ project_name }}.max_len1": "{{ max_len1 }}", | |||||
"{{ project_name }}.trim_front2": "{{ trim_front2 }}", | |||||
"{{ project_name }}.trim_tail2": "{{ trim_tail2 }}", | |||||
"{{ project_name }}.max_len2": "{{ max_len2 }}", | |||||
"{{ 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 }}.length_required1": "{{ length_required1 }}", | |||||
"{{ project_name }}.UMI": "{{ UMI }}", | |||||
"{{ project_name }}.umi_loc": "{{ umi_loc }}", | |||||
"{{ project_name }}.umi_len": "{{ umi_len }}", | |||||
"{{ project_name }}.length_required": "{{ length_required }}", | |||||
"{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}", | |||||
"{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}", | |||||
"{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}", | "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}", | ||||
"{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}", | "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}", | ||||
"{{ project_name }}.insert_size": "{{ insert_size }}", | "{{ project_name }}.insert_size": "{{ insert_size }}", |
String docker | String docker | ||||
String cluster | String cluster | ||||
String disk_size | String disk_size | ||||
String umi_loc | |||||
String trim_adapter | String trim_adapter | ||||
Int trim_front1 | |||||
Int trim_tail1 | |||||
Int max_len1 | |||||
Int trim_front2 | |||||
Int trim_tail2 | |||||
Int max_len2 | |||||
Int length_required | |||||
Int umi_len | |||||
Int qualified_quality_phred | |||||
Int length_required1 | |||||
command <<< | command <<< | ||||
nt=$(nproc) | nt=$(nproc) | ||||
cp ${read1} ${sample_id}_R1.fq.gz | cp ${read1} ${sample_id}_R1.fq.gz | ||||
cp ${read2} ${sample_id}_R2.fq.gz | cp ${read2} ${sample_id}_R2.fq.gz | ||||
else | else | ||||
fastp --thread $nt -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 ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html | |||||
fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html | |||||
fi | fi | ||||
>>> | >>> | ||||
String fastp_cluster | String fastp_cluster | ||||
String adapter_sequence | String adapter_sequence | ||||
String adapter_sequence_r2 | String adapter_sequence_r2 | ||||
String umi_loc | |||||
String hisat2_docker | String hisat2_docker | ||||
String hisat2_cluster | String hisat2_cluster | ||||
String idx_prefix | String idx_prefix | ||||
String count_length | String count_length | ||||
String sample_id | String sample_id | ||||
Int trim_front1 | |||||
Int trim_tail1 | |||||
Int max_len1 | |||||
Int trim_front2 | |||||
Int trim_tail2 | |||||
Int max_len2 | |||||
Int length_required | |||||
Int umi_len | |||||
Int qualified_quality_phred | |||||
Int length_required1 | |||||
Int insert_size | Int insert_size | ||||
Boolean pre_alignment_qc | Boolean pre_alignment_qc | ||||
disk_size=disk_size, | disk_size=disk_size, | ||||
adapter_sequence=adapter_sequence, | adapter_sequence=adapter_sequence, | ||||
adapter_sequence_r2=adapter_sequence_r2, | adapter_sequence_r2=adapter_sequence_r2, | ||||
umi_loc=umi_loc, | |||||
trim_front1=trim_front1, | |||||
trim_tail1=trim_tail1, | |||||
max_len1=max_len1, | |||||
trim_front2=trim_front2, | |||||
trim_tail2=trim_tail2, | |||||
max_len2=max_len2, | |||||
length_required=length_required, | |||||
umi_len=umi_len, | |||||
qualified_quality_phred=qualified_quality_phred, | |||||
length_required1=length_required1, | |||||
trim_adapter=trim_adapter | trim_adapter=trim_adapter | ||||
} | } | ||||