For this exercise we will use the epi2me-labs/wf-human-variation pipeline. Find information on the pipeline at https://labs.epi2me.io/workflows/wf-human-variation/
...
Approximate run time: Variable depending on whether it is targeted sequencing or whole genome sequencing, as well as coverage and the individual analyses requested. For instance, a 90X human sample run (options: --snp --sv --mod --str --cnv --phased --sex male) takes less than 8h with recommended resources.
NOTE: in contrast to the nf-core/sarek pipeline that we used in session 2, the epi2me-labs/wf-human-variation pipeline runs in ‘local’ mode (needs large amount of CPUs and RAM memory), while the nf-core/sarek pipeline will use a ‘pbspro’ mode, where the pipeline will submit individual jobs to the HPC cluster and define the CPUs and memory for each task individually.
...
Once the pipeline has completed you will see the following set of output files in the ‘results’ folder:
| Code Block |
|---|
. ├── execution │ ├── report.html │ ├── timeline.html │ └── trace.txt ├── jbrowse.json ├── OPTIONAL_FILE ├── DEMOSRR17138639.flagstat.tsv ├── DEMOSRR17138639.mosdepth.global.dist.txt ├── DEMOSRR17138639.mosdepth.summary.txt ├── DEMOSRR17138639.readstats.tsv.gz ├── DEMOSRR17138639.regions.bed.gz ├── DEMOSRR17138639.stats.json ├── DEMOSRR17138639.thresholds.bed.gz ├── DEMOSRR17138639.wf-human-alignment-report.html ├── DEMOSRR17138639.wf-human-snp-report.html ├── DEMOSRR17138639.wf-human-sv-report.html ├── DEMOSRR17138639.wf_snp_clinvar.vcf ├── DEMOSRR17138639.wf_snp.vcf.gz ├── DEMOSRR17138639.wf_snp.vcf.gz.tbi ├── DEMOSRR17138639.wf_sv.vcf.gz ├──└── DEMOSRR17138639.wf_sv.vcf.gz.tbi ├── execution │ ├── report.html │ ├── timeline.html │ └── trace.txt ├── jbrowse.json └── OPTIONAL_FILE |
Let’s inspect the HTML reports for wf-human-alignment-report.html, wf-human-snp-report.htmland wf-human-sv-report.html.
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
To browse the working folder in the HPC type in the file finder:
...