shl198/salmon_quant_all repository overview

how to run this pipeline:

1. put all fastq files into a folder. make sure the fastq file is compressed in gz format. and if it's single end read, the file name should ends with _1.fq.gz; if they are paired end reads, then the file names should be _1.fq.gz, _2.fq.gz
2. in terminal run: docker run -v /path/to/fq/files:/data shl198/salmon_quant_all