Release: 5.0.0 Green Squirrel #864
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Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
nf-test: default config
Skip short and long read qc
Fix docs typo
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
New config test_single_end
…d by the tool" This reverts commit 69a955e.
conf/modules.config
Outdated
| "--min_af ${params.gtdbtk_min_af}", | ||
| "--pplacer_cpus ${params.gtdbtk_pplacer_cpus}", | ||
| params.gtdbtk_use_full_tree ? "-f" : "", | ||
| "--skip_ani_screen", |
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I would not put this in the general modules.config file, as this disables ANI screening for fast genome classification using skani (I think the fact it was set if the mash db wasn't provided was actually a bug with the old version of the module).
Maybe better to make a param for it (default false) and set it to true in the tests?
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Or other way round skip and we set to true in our config?
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We have params.gtdbtk_use_full_tree, how about params.gtdbtk_skip_ani_screen?
Set to false by default, but true in test.config?
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OK I think I've implemented what you suggested
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Let me know If I did that properly
Co-authored-by: Jim Downie <[email protected]>
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@nf-core-bot fix linting |
…dmundmiller hack to get SPADES to work on Fusion
…re on exit code 1 for MAG_DEPTHS_PLOTS,
…ue to summarise problem
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).