Alignment subworkflows
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enhancement
good-first-issue
- Dominant language
- Nextflow
- Stars
- 63
- Forks
- 39
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
Instead of using modules for the alignment step, use the nf-core subworkflows.
- Use fastq_align_bwa for BWA alignment
- Use fastq_align_bowtie2 for bowtie2 alignemnt
- Create and use a new subworkflow for minimap2 alignment
- Once we have Samtools stats we can also add these to the MultiQC report
** Consider creating a subworkflow with indexing + the respective alignment subworkflows
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 by locating the existing alignment modules and the pipeline entry points that call them. Read the linked fastq_align_bwa and fastq_align_bowtie2 subworkflows, then determine how a new minimap2 subworkflow and indexing wrapper fit alongside them. Done means all three aligners use subworkflows and Samtools statistics are included in the MultiQC report.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100