Instead of merging fastq files as the first step of the pipeline, merge
as late as possible to make better use of parallelism, and to prevent
unnecessary reading/writing of all data. Currently, reads are trimmed
and mapped per read group, and are merge in the picard MarkDuplicates
step. Therefore, samples are merged as a side effect of another task
that was performed as well.

Additionally, fastq processing is now done in a single step using
cutadapt, instead of using both sickle and cutadapt sequentially.

As part of these changes, the following changes were made:
 - Use cutadapt to trim both adapters and low quality reads
 - Run bwa align on each readgroup independently
 - Run fastqc on each readgroup independenly
 - Pass multiple bam files to picard MarkDuplicates
 - Remove safe_fastqc.sh script
 - Remove fastqc_stats
 - Remove fastqc coverage from covstats
 - Update test data for slight differences in output vcf files
 - Add tests for fastqc zip files