Pass file to cutadapt
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- Dominant language
- Nextflow
- Stars
- 63
- Forks
- 39
- PR merge metrics
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Description
Description of feature
Thanks for developing this useful pipeline.
I was wondering if it's possible to run the screening pipeline with cutadapt specifying fasta file of multiple adaptor sequences e.g. like here. I have tried trying to pass --cutadapt file:adapters.fasta to the nextflow pipeline, however, I receive an error stating that the 'adapters.fasta' file cannot be found, even though it is there locally.
I am running nextflow version 23.10.1, crisprseq v2.1.1, with singularity as a profile.
Thanks for your help.
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 the screening pipeline's --cutadapt parameter and how adapters.fasta is passed to the cutadapt process; the issue names no repository files or tests. Check the pipeline's file-input handling with the provided multi-sequence adapters.fasta under the Singularity profile. Done means a local adapter FASTA can be supplied and used successfully.
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