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remove fastp useless paramater

tags/v0.1.0
stead99 vor 4 Jahren
Ursprung
Commit
b7bda92886
4 geänderte Dateien mit 1 neuen und 60 gelöschten Zeilen
  1. +0
    -12
      defaults
  2. +0
    -14
      inputs
  3. +1
    -12
      tasks/fastp.wdl
  4. +0
    -22
      workflow.wdl

+ 0
- 12
defaults Datei anzeigen

"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",

+ 0
- 14
inputs Datei anzeigen

"{{ 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 }}",

+ 1
- 12
tasks/fastp.wdl Datei anzeigen

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
>>> >>>

+ 0
- 22
workflow.wdl Datei anzeigen

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
} }

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