BioContainer pipeline

• Build a pipeline create transcript level count matrix from SRR file only with Biocontainers
• This pipeline can be used any environment containing docker/docker-compse. (Win/Mac/Linux)

Dir structure

Biocontainers
|--Dockerfiles
|--input
|--output
|--STARidx
|--docker-components
|		|- docker-compose-XXX.yml
|		|-.env
|--wait-for-it.sh

Overall flow

• All processes are cotroled in docker-compose.yml
• wait-for-it.sh dominates the run order of containers written in docker-compose

SRR file
↓ 1.(parallel-fastq-dump)
FastQ 
↓ 2.(fastp)
FastQ (quarity checked.trimed)
↓ 3.(STAR)
BAM/SAM
↓ 4.(RSEM)
count data

Usage

1. create docker image for RSEM

docker build -t biocontainer/rsem -f Dockerfiles/rsem

2. Create STAR index (refer to this section )
3. Create RSEM index (refer to this section)
4. Modify variables in .env

All run

make all

Each tool run

• This repository has docker-compose-XXX.yml file for each bioinformatics tools
  • XXX: sratoolkit,fastq-dump,fastp,STAR,RSEM
• Each tools can be run independently with below command

make ${TOOL_NAME}