Fixed == which should have been eq

Even though they're currently commented out, I fixed this bug :P
Switched to using modulecmd perl to load modules. Removed environment module path config variable.
Added -q quiet to fastqc to suppress percentages in CF report.
Removed scoping error which was breaking download dependencies.
Stopped CF from trying to load a module if it's already been loaded.
Corrected typo in module dependency list for bismark_align
New code to tidy up log files, reordering stdout by module. Untested.
Made the output log reordering code work.
Added environment module dependencies to bismark cf modules.
Fixed SLURM --qstat problems where the order of squeue meant some stuff was being missed off..
Added FastQC flag -q to Trim Galore! module
Tweaks to the run finished module.
Removed the bismark_tidy module and renamed bismark_messy to bismark_report.
Updated references to bismark_report in a few pipelines that I had missed
Implemented environment module aliases.
Updated readme with changelog mentioning bismark_tidy removal and env module alias addition
Added code to prevent run_finished and pipeline_finished from adding job id line prefixes.
First draft of nice HTML status e-mails
Attempt at a fix for the broken e-mail in cf_runs_all_finished.cfmod
Moved environment module loading into a function in Helpers.pm. is_bam_paired_end now load samtools