This workflow is replicate the QA protocol implemented at JGI for Illumina reads and use the program “rqcfilter2” from BBTools(38:44) which implements them as a pipeline.

• RQCFilterData Database: It is a 106G tar file includes reference datasets of artifacts, adapters, contaminants, phiX genome, host genomes.

• Prepare the Database

	mkdir -p refdata
	wget https://portal.nersc.gov/cfs/m3408/db/RQCFilterData.tgz
	tar xvzf RQCFilterData.tgz -C refdata
	rm RQCFilterData.tgz

Description of the files:

• .wdl file: the WDL file for workflow definition
• .json file: the example input for the workflow
• .conf file: the conf file for running Cromwell.
• .sh file: the shell script for running the example workflow

microbiomedata/bbtools:38.44

1. database path,
2. fastq (illumina paired-end interleaved fastq),
3. output path
4. memory (optional) ex: "jgi_rqcfilter.memory": "35G"
5. threads (optional) ex: "jgi_rqcfilter.threads": "16"

{
    "jgi_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database", 
    "jgi_rqcfilter.input_files": [
        "/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz", 
        "/global/cfs/cdirs/m3408/ficus/8434.1.102069.ACAGTG.fastq.gz", 
        "/global/cfs/cdirs/m3408/ficus/8434.3.102077.ATGTCA.fastq.gz"
    ], 
    "jgi_rqcfilter.outdir": "/global/cfs/cdirs/m3408/ficus_rqcfiltered"
}

The output will have one directory named by prefix of the fastq input file and a bunch of output files, including statistical numbers, status log and a shell script to reproduce the steps etc.

The main QC fastq output is named by prefix.anqdpht.fast.gz.

|-- 8434.1.102069.ACAGTG.anqdpht.fastq.gz
|-- filterStats.txt
|-- filterStats.json
|-- filterStats2.txt
|-- adaptersDetected.fa
|-- reproduce.sh
|-- spikein.fq.gz
|-- status.log
|-- ...