Simplify object management

[realmichaelhoffert]

As of 1.14, DADA2 now supports passing directories rather than paths to functions:

Directories containing fastq files (possibly compressed) can now be provided to core dada2 functions instead of a character
vector of the fastq filenames. This functionality is supported by filterAndTrim, learnErrors, dada, mergePairs and derepFastq.
Note, this feature requires fastqs in the provided directory to have standard file extensions: .fastq, .fastq.gz or .fastq.bz2. 

This makes a lot of the pipeline code to organize filepaths and copy files between different locations unnecessary. We could reduce the number of required lines of code and also make the process of running a dataset simpler.

[](https://github.com/fiererlab/dada2_fiererlab#1-filter-and-trim-for-quality)# Put filtered reads into separate sub-directories for big data workflow
dir.create(filter.fp)
    subF.fp <- file.path(filter.fp, "preprocessed_F") 
    subR.fp <- file.path(filter.fp, "preprocessed_R") 
dir.create(subF.fp)
dir.create(subR.fp)

# Move R1 and R2 from trimmed to separate forward/reverse sub-directories
fnFs.Q <- file.path(subF.fp,  basename(fnFs)) 
fnRs.Q <- file.path(subR.fp,  basename(fnRs))
file.rename(from = fnFs.cut, to = fnFs.Q)
##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
file.rename(from = fnRs.cut, to = fnRs.Q)
##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

# File parsing; create file names and make sure that forward and reverse files match
filtpathF <- file.path(subF.fp, "filtered") # files go into preprocessed_F/filtered/
filtpathR <- file.path(subR.fp, "filtered") # ...
fastqFs <- sort(list.files(subF.fp, pattern="fastq.gz"))
fastqRs <- sort(list.files(subR.fp, pattern="fastq.gz"))
if(length(fastqFs) != length(fastqRs)) stop("Forward and reverse files do not match.")

[cliffbueno]

I am not going to implement this is Version 2.0.0. Our current file system is working just fine so don't think it's super urgent to implement this. We'll leave the enhancement tag on it and it could be something to implement in version 3.0.0 down the road.