Integration of Parabricks
Open
Nobody has claimed this yet.
enhancement
new module
sarek
- Dominant language
- Nextflow
- Stars
- 429
- Forks
- 1.1k
- Avg merge
- 1d 6h
- Merged PRs (30d)
- 153
Description
This Issue is to track which Parabricks tools are available as nf-core modules.
Source: Parabricks documentation
Before working on a new Parabricks module, please create and link the GitHub Issue below:
Alignment
- fq2bam (bwa-mem) https://github.com/nf-core/modules/issues/3983
- fq2bam_meth https://github.com/nf-core/modules/issues/6739
- giraffe
- minimap2 https://github.com/nf-core/modules/issues/8626
- STAR (rna_fq2bam) https://github.com/nf-core/modules/issues/8785
Preprocessing
- applybqsr https://github.com/nf-core/modules/issues/6861
- bam2fq
- bqsr
- bamsort
- markdup
Variant Calling
- deepsomatic
- deepvariant
- haplotypecaller
- mutectcaller
- starfusion https://github.com/nf-core/modules/issues/9133
Quality Checks
- bammetrics
- collectmultiple metrics
GVCF Processing
- indexgvcf
- dbsnp
- genotypegvcf
- prepon
- postpon
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the unchecked Parabricks tools in the Alignment, Preprocessing, Variant Calling, Quality Checks, and GVCF Processing lists, and review the linked module issues for the completed entries. For any new module, follow the issue's instruction to create and link a separate GitHub issue; this tracker is complete when each listed tool is checked or has an associated issue.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100