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Pipeline summary report #558
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Curiously with |
…tion was performed
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https://github.com/tillenglert/ampliseq/blob/b193c0f2cddde67d4759662cb269c8c521916b52/assets/report_template.Rmd#L194 These lines will cause issues after merging with dev ( |
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Some comments already
max_disc <- round( 100 - min(passed_col), 1 ) | ||
avg_passed <- round(mean(passed_col),1) | ||
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cutadapt_text_unch <- "Primers were trimmed using cutadapt" |
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Maybe this sentence can be omitted if the flag retain untrimmed is set.
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I would argue that even if untrimmed are retained, the trimming was attempted and therefore that text snippet is fine I think.
Co-authored-by: Till E. <[email protected]>
…e/summary_report
Co-authored-by: Till E. <[email protected]>
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Approving here. Code was written by 2 devs and reviewed by a third.
The product of that addition, the pipeline summary report itself, was also reviewed several times by multiple people. While its never finished, it seems in a good state to be added to the pipeline imho.
This PR adds a report module to the nf-core/ampliseq Pipeline. The report should include short text snippets for each module and either graphs or tables depicting the output of the corresponding tool.
The report is written in Rmarkdown and is generated using an external R script using a template .Rmd file. It is still work in progress, as I first wrote everything to be working on the results directory. Currently I'm adding each individual file which is used in the report to the input of the module, R script and into the template.
This draft PR should also enable @d4straub to help me when he has some time.
(Second PR as the first one was a bit messy.)
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).