---
title: "cutadapt.wrapper"
author: "Moncho"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output: html_document
params:
  folder: 
    value: ../data_sub/fastqs
  metadata:
    value: ../data_sub/metadata.csv
  outputfolder:
    value: ../test
  minlength:
    value: 100
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Cutadapt wrapper

This is an R Markdown document. It is just a means to passing the parameters from the metadata file into a bash script

## Step0: Check the metadata colnames.

The minimum info needed must have the following column names:

        - Sample_name - The name that makes sense to you and your project (No spaces in the name would be better)
        - Locus: The name of the locus you want to use (e.g. Leray_COI)
        - PrimerF: The nucleotide sequence of the forward primer - supports IUPAC characters 
        - PrimerR: Ditto for the reverse primer (also in 5' -> 3' direction)
        - file1: it should match exactly the output of the Miseq.
        - file2: Same for the second read.
        
Does not matter if you youbring more columns - good. But these are the minimum

## Step1: Params into a file for your records

```{r}
dir.create(params$outputfolder)

library(tidyverse)

tibble(values = as.character(params), names = as.character(names(params))) %>% 
  pivot_wider(names_from = names,
              values_from = values) %>%
  select(folder, metadata, outputfolder, minlength) %>% 
write_csv( "params.txt" )


```

```{bash}
cutadapt --version
```


```{bash}

bash test.bash.sh params.txt
```