QC pipeline Dev - dna alignment QC workflow in nf-core framework

[lindaxiang]

First iteration of the workflow: https://github.com/icgc-argo-workflows/dnaalnqc Presented on May 26th QC working group meeting and got some feedback, will adjust the workflow to:

• accept both normal/tumour paired and tumour-only alignments as inputs
• report sample level contamination

[edsu7]

• add off-target read metric for targeted sequencing

[lindaxiang]

Benchmark resource

• GA4GH benchmark datasets: 100 samples BAM https://github.com/ga4gh/quality-control-wgs/blob/main/benchmark_resources/n.100-1kg-dragen3.7.6-bam.csv
• GA4GH reference implementation of the standards: https://github.com/c-BIG/NPM-sample-qc
• GA4GH benchmark results: https://github.com/ga4gh/quality-control-wgs/tree/feature/benchmark-results/benchmark_resources/n.100-1kg-dragen3.7.8-npm-sample-qc-results

Running the ARGO dnaalnqc workflow with inputs from the same benchmark datasets, and will compare the following metrics with GA4GH's benchmark results:

• yield_bp_q30
• mean_autosome_coverage
• pct_autosomes_15x
• mad_autosome_coverage
• pct_reads_mapped
• pct_reads_properly_paired
• mean_insert_size
• insert_size_std_deviation
• cross_contamination_rate

[lindaxiang]

Test the workflow in RDPC-QA and the run completed successfully: https://wes.rdpc-qa.cancercollaboratory.org/runs/wes-3f7cdfe35468484491e2f42e1964008d

[lindaxiang]

Next steps:

• [x] - update the payload/qcmetrics module (updated module PR is under review) and make PR after.
• [x] - depend on payload schema change: https://github.com/icgc-argo/argo-metadata-schemas/issues/78
• [ ] - test it in cumulus rdpc