Add EDAM ontologies
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 23
- Forks
- 6
- Avg merge
- 1d 9h
- Merged PRs (30d)
- 6
Description
Description of feature
Add ontologies for every modules used in the references pipeline:
- bbmap/bbsplit
- bowtie/build
- bowtie2/build
- bwa/index - https://github.com/nf-core/modules/pull/7524
- bwamem2/index - https://github.com/nf-core/modules/pull/7524
- custom/catadditionalfasta
- dragmap/hashtable
- gatk4/createsequencedictionary
- gawk
- gffread
- gunzip
- hisat2/build
- hisat2/extractsplicesites
- kallisto/index
- msisensorpro/scan
- multiqc
- rsem/preparereference
- salmon/index
- samtools/faidx
- sortmerna
- star/genomegenerate
- tabix/bgziptabix
- tabix/tabix
- untar
- unzip
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
The issue provides a checklist of reference-pipeline modules but names no files, tests, or implementation entry points. Start by locating how the existing bwa/index and bwamem2/index ontologies were added, using the linked pull request as the reference, then work through the unchecked modules. Done means each unchecked module has an ontology and the checklist can be completed.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100