kosarhooshmand / sra-rnaseq

✒️SRA-RNAseq

My Guthub repo include pipelines for running Pre-processing methods such as Trimming, quality control and pseudoalignment on SRA fastq files using Trimmomatic, fastQC and Kallisto tools respectively . All the pipelines are written using the Workflow Description Language (WDL) and can be executed using Cromwell and Docker.

⚙️Technologies & Tools

🔗 Quick Start

SRA fastq files download

• Install SRAtoolkit
• Run the following command to download SRA fastq files in parallel. The list.txt includes SRA ids.

parallel --jobs n "fastq-dump --split-files --skip-technical -B --gzip {}" :::: list.txt

Running Trim-QC & Kallisto pipeline in WDL format

• Install JAVA, and Cromwell
• Build Docker images for Trimmomatic, fastQC and Kallisto
• For running Kallisto.wdl you also need to build an index from a FASTA formatted file of target sequences using Kallisto and name it under gencode.idx.
• Run the workflow directly by executing the following commands on your terminal:

java -Dconfig.file=application.conf -jar cromwell-55.jar run Trim-QC.wdl -i Trim-QC.json

java -Dconfig.file=application.conf -jar cromwell-55.jar run Kallisto.wdl -i Kallisto.json