VCF2Genome

[jfy133]

Adds consensus sequence generation step with VCF2Genome, to reach parity with EAGER2.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Usage Documentation in docs/usage.md is updated
• Output Documentation in docs/output.md is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Once this is merged here: bioconda/bioconda-recipes#19087

We can update the code basis as the CLI changed a small bit (doesn't need the . for current directory anymore. Also adds in a Version: 0.6 string in the help, which means we can update the scrape software versions.

Need to bump the environment once this is merged to get it passing here in tests too :-) Can you open a separate PR for updating once the above PR is merged @jfy133 ?

[apeltzer]

Also:

1s
##[error]Process completed with exit code 1.
Run markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
/home/runner/work/eager/eager/docs/usage.md:728 MD018/no-missing-space-atx No space after hash on atx style heading [Context: "###`--vcf2genome_outfile`"]
/home/runner/work/eager/eager/docs/usage.md:730 MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]
/home/runner/work/eager/eager/docs/usage.md:732 MD018/no-missing-space-atx No space after hash on atx style heading [Context: "###`--vcf2genome_header`"]
/home/runner/work/eager/eager/docs/usage.md:736 MD018/no-missing-space-atx No space after hash on atx style heading [Context: "###`--vcf2genome_minc`"]
/home/runner/work/eager/eager/docs/usage.md:740 MD018/no-missing-space-atx No space after hash on atx style heading [Context: "###`--vcf2genome_minq`"]
/home/runner/work/eager/eager/docs/usage.md:744 MD018/no-missing-space-atx No space after hash on atx style heading [Context: "###`--vcf2genome_minfreq`"]
##[error]Process completed with exit code 1.

[jfy133]

Once this is merged here: bioconda/bioconda-recipes#19087

We can update the code basis as the CLI changed a small bit (doesn't need the . for current directory anymore. Also adds in a Version: 0.6 string in the help, which means we can update the scrape software versions.

Need to bump the environment once this is merged to get it passing here in tests too :-) Can you open a separate PR for updating once the above PR is merged @jfy133 ?

Yup will do. PR with complete VCF2Genome coming up in a few minutes (with correctd linting). Will update the MtNucRatio after in the morning when it bioconda should be merged.

[maxulysse]

Looks good.