nextflow_schema.json: Any of --fasta or --genome#471
Open
suhrig wants to merge 1 commit intonf-core:devfrom
Open
nextflow_schema.json: Any of --fasta or --genome#471suhrig wants to merge 1 commit intonf-core:devfrom
nextflow_schema.json: Any of --fasta or --genome#471suhrig wants to merge 1 commit intonf-core:devfrom
Conversation
Member
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
When the pipeline is launched with the parameter
--genomeset, the FastA file is normally obtained from theigenomes.configfile. However, the pipeline complains that--fastais not set in this situation. This PR changes the parameter validation to require that only--genomeor--fastabe set.Note: Linting currently fails with
FileNotFoundError: [Errno 2] No such file or directory: 'tests/nextflow.config', but this has nothing to do with this PR.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.CHANGELOG.mdis updated.