wdl-fastqc's Introduction

wdl-fastqc

A high throughput sequence QC analysis tool

Setup

The pipeline is a part of SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.

Create Job Files

You need two files to run the FastQC pipeline - one inputs file and one labels file. Use the following example files to help you create your job file:

config/template.inputs.json
config/template.labels.json

Submitting a Job

conda activate scing

./submit.sh \
    -k ~/keys/cromwell-secrets.json \
    -i configs/sample.inputs.json \
    -l configs/sample.labels.json \
    -o FastQC.options.aws.json

Helper Utilities

$ ./get-fastq-list-from-s3.sh \
    -p s3://dp-lab-data/collaborators/lowe/p53_loss_enrichment/Preclinical_SP_batch1/genomic/

s3://dp-lab-data/collaborators/lowe/p53_loss_enrichment/Preclinical_SP_batch1/genomic/1740_Preclinical_SP_batch1_IGO_10682_11_S11_L001_R2_001.fastq.gz
s3://dp-lab-data/collaborators/lowe/p53_loss_enrichment/Preclinical_SP_batch1/genomic/1740_Preclinical_SP_batch1_IGO_10682_11_S11_L002_R2_001.fastq.gz

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