Inconsistent output file locations between modules

[jfy133]

Describe the bug
Structuring of final output files are not consistent.

For example: damageProfiler, dedup, bwa, qualimap, samtools either have sample specific directories (so all module output files related to that sample are placed in this directory). Or have all files from all samples in a single output directory. Either is fine IMO

However read_merging, fastqc both have some files of one sample in one directory, and other files of the same sample in a parent directory etc (i.e. not placed together). Further, stripped_fastq is under the samtools output directory, despite being a separate module. More specifically:

• preAR FASTQC 'raw' files (zips directory/html) are just in FastQC/, whereas post-AR are in a FastQC/after_clipping/ directory. The former should be e.g. placed in a before_clipping directory for consistency.
• For read_merging/ the actual output FASTQ files are in read_merging/output/ whereas the settings log files are in the parent read_merging/. the FASTQ and .settings files should be placed in the same place.
• stripped_fastq output directory should be in the parent output directory, not under samtools/

To Reproduce
Run EAGER (current version is -r dev on 2019-05-04).

Expected behaviour
For consistency, and make it intuitive for users to find output files, multi-sample runs should have the same folder/file structure per module.

[jfy133]

I realise now that actually the output directories per sample is either program specific, or when the output files of multiple samples may result in duplicate file names (e.g. dedup.log).

A user should be familiar enough with the program (or know where ot look for documentation) to understand this, so I guess this isn't necessary for the moment.