Update documentation for v2.0.0 #166
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…crash in tumor only mode
…iguration' heading/section
… sectio 'container images'
…ction 'why lilac crashes on panel sample', add section 'automatically increases compute resources'
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 2.14.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Hi all, i've now completed the documentation for OA v2.0.0. For this PR, we only need to consider the files in |
| only be used for [tuning process resource | ||
| specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such | ||
| as output directories), or module arguments (args). | ||
| To run from CRAM, simply provide the CRAM and/or CRAM index to `bam`/`bai` ibn column `filetype`: |
| equivalence of these two pieces of software. The functional/feature parity with regards to version releases are detailed | ||
| in the below table. | ||
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| | oncoanalyser | hmftools | |
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Shouldn't this stay in ?
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We agreed hartwig pipeline / hmftools updates will be tied to an oncoanalyser version. So no need for section 'release parity'
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| The default settings of `oncoanalyser` will accommodate typical sequencing depths for sample inputs and each individual | ||
| tool is generally sequencing depth agnostic. However, variant calling is optimised for 100x tumor and 40x normal when | ||
| invoked in `wgts` mode and expects sparse high-depth read data characteristic of panel sequencing when run in `targeted` |
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I think this could benefit from staying in?
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Restored this note
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| ### Running `oncoanalyser` offline |
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Actually, the way to do this is using the nf-core download (using the nf-core python package) command which will also download all the container images etc and you can copy that file in your HPC and run offline from there
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Moving documentation changes over into #181 to avoid having to merge these conflicts |
PR checklist
nf-core 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).