ICGC ARGO Pre Alignment QC Workflow

This repository maintains the source code of the ICGC ARGO Pre Alignment QC Workflow for DNA/RNA Seq. The workflow is written in Nextflow workflow language using DSLv2, with modules imported from other ICGC ARGO GitHub repositories. Specifically, here are repositories maintaining various of tools/modules:

• https://github.com/icgc-argo-workflows/argo-qc-tools
• https://github.com/icgc-argo-workflows/dna-seq-processing-tools
• https://github.com/icgc-argo-workflows/data-processing-utility-tools
• https://github.com/icgc-argo-workflows/nextflow-dna-seq-processing-tools

Each Nextflow module (including associated container image which is registered in ghcr.io) is strictly version controlled and released independently. To ensure reproducibility the pipeline declares explicitly which specific version of a module is to be imported.

Major tasks performed in the workflow

• download input sequencing metadata/data from data center using SONG/SCORE client tools
• preprocess input sequencing reads (in FASTQ or BAM) into FASTQ file(s) per read group
• perform FastQC analysis for FASTQ file(s) per read group
• perform Cutadapt analysis for FASTQ file(s) per read group
• perform MultiQC analysis to generate aggregated results
• generate SONG metadata for all collected QC metrics files and upload them to SONG/SCORE

Inputs

Local mode

• study_id
• analysis_metadata
• sequencing_files

RDPC mode

• study_id
• analysis_id
• song_url
• score_url
• api_token

Outputs

• file_pair_map: CSV file with each row contains 3 columns: read_group_id, file_r1, file_r2, which represent information for each read group
• payload: Payload contains metadata for all QC files
• multiqc_report: HTML report file multiqc_report.html

Run the pipeline

To run the pipeline, please follow instruction here to install Nextflow (version 20.10 or higher) first. With inputs prepared, you should be able to run the workflow using the following command. Please replace the params file with a real one (with all required parameters and input files). Example params file example-params.json can be found in the workflow root folder.

Run 0.1.0 version of the pipeline:

nextflow run icgc-argo-workflows/pre-alignment-qc/main.nf -r 0.1.0 -params-file <your_params_file.json>

You may need to run nextflow pull https://github.com/icgc-argo-workflows/pre-alignment-qc if the version 0.1.0 is new since last time the pipeline was run.

Please note that SONG/SCORE services need to be available and you have appropriate API token.