lizhihui
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rnaseq_fastp
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rnaseq_fastp/inputs

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  1. {

  2.     "{{ project_name }}.sample_id": "{{ sample_id }}",

  3.     "{{ project_name }}.read1": "{{ read1 }}",

  4.     "{{ project_name }}.read2": "{{ read2 }}",

  5.     "{{ project_name }}.idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",

  6.     "{{ project_name }}.gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",

  7.     "{{ project_name }}.idx_prefix": "genome_snp_tran",

  8.     "{{ project_name }}.hisat2.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.0.5-1-deb-cv1",

  9.     "{{ project_name }}.hisat2.cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  10.     "{{ project_name }}.samtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

  11.     "{{ project_name }}.samtools.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  12.     "{{ project_name }}.stringtie.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",

  13.     "{{ project_name }}.stringtie.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  14.     "{{ project_name }}.fastp.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",

  15.     "{{ project_name }}.fastp.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  16.     "{{ project_name }}.adapter_sequence": "{{ adapter_sequence if adapter_sequence != '' else 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' }}",

  17.     "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 if adapter_sequence_r2 != '' else 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' }}"

  18. }