nf-core / nf-core/seqinspector
Allow fastqscreen inputs to just be a fasta
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 28
- Forks
- 44
- Avg merge
- 11d 8h
- Merged PRs (30d)
- 2
Description
Description of feature
Kinda similar to #21.
I wish I could do:
name,dir,basename,aligner
Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/genome.fa,genome,bowtie2
And the workflow would build the reference for me on the fly as well.
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 tracing how fastqscreen inputs and references are currently handled, then compare the requested behavior with issue #21. Use the example FASTA and S3 input to define the expected workflow, including successful on-the-fly reference construction and fastqscreen execution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- aws
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100