report.Rmd

---
title: "Hydra report"
author:
- "Mattias  de Hollander (m.dehollander@nioo.knaw.nl)"
date: "`r format(Sys.time(), '%d %B, %Y')`"
params:
    rmd: "report.Rmd"
output:
  html_document:
    highlight: tango
    number_sections: no
    theme: default
    toc: yes
    toc_depth: 3
    toc_float:
      collapsed: no
      smooth_scroll: yes
bibliography: ../../hydra.bib
link-citations: true
---
# Hydra report for `r snakemake@config$project`

## Workflow details

- Hydra pipeline version 1.3.3 [@hollander_nioo-knaw/hydra:_2017] implemented in Snakemake [@koster_snakemakescalable_2012].
- Quality control: BBDuk2 from the BBMap tool suite [@bushnell_bbmap_2015]. 
- Read merging:`r if (snakemake@params[["mergemethod"]] == "vsearch") "Fastq_mergeparis option of vsearch [@rognes_vsearch:_2016]" else if (snakemake@params[["mergemethod"]] == "pandaseq") "Pandaseq [@masella_pandaseq:_2012]"` 
- `r if (snakemake@config$its) "The ITS2 region is extracted using ITSx version 1.011 [@bengtsson-palme_improved_2013]."`
- Clustering: `r if (snakemake@config$clustering == "usearch_smallmem") "smallmem algorithm [@edgar_search_2010] as implented in vsearch."`
- Chimera's:  UCHIME algorithm in de-novo mode [@edgar_uchime_2011] implemented in VSEARCH. 
- Mapping: usearch_global method implemented in VSEARCH to create an otutable and converted to BIOM-Format [@mcdonald_biological_2012].
- Taxonomy: `r if (snakemake@config$classification == "sina") "aligning the sequences to the SILVA database (release 132) [@quast_silva_2013] using SINA [@pruesse_sina:_2012]" else if (snakemake@config$classification == "stampa") paste("aligning the sequences to the SILVA database (release 128) [@quast_silva_2013]. First the references sequences are trimmed with the forward (", snakemake@config$forward_primer, ") and reverse(", snakemake@config$reverse_primer, ") primer using cutadapt [@martin_cutadapt_2011]. Next, sequences are aligned using the usearch_global method implemented in vsearch. At last, the last common ancestor taxonomy is determined for the top hits using a python script provided by STAMPA [@mahe_stampa:_2017]") else if (snakemake@config$classification == "rdp") "running the RDP Classifier re-trained on the UNITE database release 7.2[@koljalg_towards_2013]" else if (snakemake@config$classification == "blast") paste("running BLASTN against the", snakemake@config$blast_db, "database and taking the least common ancestor of the top", snakemake@config$blast_max_hits, "hits.")`.

## Workflow overview
![](`r paste(snakemake@scriptdir, snakemake@input$workflow, sep="/")`)

### Input files

```{r kable, message=FALSE, warning=FALSE}
library(knitr)
kable(snakemake@config$data)
```

### Read counts

```{r readstats, message=FALSE, warning=FALSE}
library(knitr)
kable(read.delim(snakemake@input$readstat))
```

## Downloads
<!--<script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script>-->
<script>
function download(text, id, name, type) {
  var file = new Blob([text], {type: type})
  var a = $(id)
  a[0].href = URL.createObjectURL(file)
  a[0].download = name
}
function dataURItoBlob(dataURI, callback) {
    // convert base64 to raw binary data held in a string
    // doesn't handle URLEncoded DataURIs - see SO answer #6850276 for code that does this
    var byteString = atob(dataURI.split(',')[1]);

    // separate out the mime component
    var mimeString = dataURI.split(',')[0].split(':')[1].split(';')[0]

    // write the bytes of the string to an ArrayBuffer
    var ab = new ArrayBuffer(byteString.length);
    var ia = new Uint8Array(ab);
    for (var i = 0; i < byteString.length; i++) {
        ia[i] = byteString.charCodeAt(i);
    }

    // write the ArrayBuffer to a blob, and you're done
    var bb = new Blob([ab]);
    return bb;
}
</script>

<p><a id="biom" href="link">Download BIOM file</a></p>
<script>
dataURL = "`r base64enc::dataURI(file = snakemake@input$biom, mime = 'text/csv', encoding = 'base64')`"

download(dataURItoBlob(dataURL), "#biom", "`r basename(snakemake@input$biom)`", 'text/plain')
</script>

<p><a id="otutable" href="link">Download otutable in txt format</a></p>
<script>
dataURL = "`r base64enc::dataURI(file = snakemake@input$otutable, mime = 'text/csv', encoding = 'base64')`"

download(dataURItoBlob(dataURL), "#otutable", "`r basename(snakemake@input$otutable)`", 'text/plain')
</script>

<p><a id="otus" href="link">Download OTUs in FASTA format</a></p>
<script>
dataURL = "`r base64enc::dataURI(file = snakemake@input$otus, mime = 'text/csv', encoding = 'base64')`"

download(dataURItoBlob(dataURL), "#otus", "`r basename(snakemake@input$otus)`", 'text/plain')
</script>


<a download="readstat.csv" href="`r base64enc::dataURI(file = snakemake@input$readstat, mime = 'text/csv', encoding = 'base64')`">Readstat csv file</a>

<a download="report.Rmd" href="`r base64enc::dataURI(file = params$rmd, mime = 'text/rmd', encoding = 'base64')`">R Markdown source file (to produce this document)</a>

## References