RNA-seq pipeline with tophat2 + cufflinks + trimmomatic + fastqc
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README.md

Arguments

# User Defined
read1: oss://pgx-storage-results/demo/Quartet-RNA-D5-3-test.clipped_R1.fastq.gz
read2: oss://pgx-storage-results/demo/Quartet-RNA-D5-3-test.clipped_R2.fastq.gz
baseout: Quartet-RNA-D5-3-test.clipped
idx_prefix: genome
genome_directory: oss://pgx-storage-results/yangjingcheng/reference/genome/
gtf: oss://pgx-storage-results/yangjingcheng/reference/genome/genes.gtf
adapter: oss://pgx-storage-results/yangjingcheng/reference/illumina_adapter/TruSeq3-PE.fa

# Default Value
fastqc_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5
trimmomatic_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8
tophat2_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat2:2.0.14
cuffdiff2_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1