Enhancing documentation for viral-pipelines #461
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…eplete and classify_single
.vscode/settings.json
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delete this file from the branch and perhaps add .vscode/ to the .gitignore file instead?
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One quick note: I went into readthedocs and activated automatic public builds of the See here for rendered output: https://viral-pipelines.readthedocs.io/en/fnegrete_test/ See here for build status (right now it's succeeding so nothing to see here, but if for some reason you had a syntax error or something, you'd see failures here): https://readthedocs.org/projects/viral-pipelines/builds/ |
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
Co-authored-by: Daniel Park <dpark@broadinstitute.org>
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Did we merge this? Should I keep it open for future documentation fixes? |
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amplicon16S analysis wdl renamed to classify_qiime2_multi Noticed that the old name is on the master branch still, so we should updated this |
| cateogry: "advanced" | ||
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| min_length: { | ||
| description: "Minimum length of the read, cutadapt will discard anything that is shorter than n bp AFTER trimming.Set to default.", |
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Whose default? qiime's? cutadapt's? Maybe specify the source of the default and/or its value here. Also maybe specify that it would be reads that would be discarded: "discard anything that is" -> "discard reads that are". If such reads are discarded, does that extend to both reads of a pair for paired-end sequencing, or could it toss one read and keep its mate?
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After this small change, let's get this merged in.
| cateogry: "advanced" | ||
| } | ||
| min_length: { | ||
| description: "Minimum length of the read, cutadapt will discard anything that is shorter than n bp AFTER trimming.Set to default.", |
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After this small change, let's get this merged in.
Adding documentation to important input/ouput parameters for some of the more used workflows in the pipeline (assembled_refbased, demux_deplete,classify_single, augur_from_assemblies, and genbank.
Additionally orphan workflows will be noted.