Support multiple sample inputs: SRA ids, s3/local directories of fastq files, or samples.csv

[olgabot]

This PR extends main.nf to allow for multiple possible ways to specify samples:

• SRA ids, i.e individual SRR ids or entire SRP or PRJNA project files
• S3 or local directories containing R1, R2 read pairs
• samples.csv file with the headers sample_id,read1,read2

[olgabot]

Still can't get this to properly support 3 different input types. Some how the concatenation of channels is wonky: https://groups.google.com/forum/#!topic/nextflow/KSUFJvbIzGE

[olgabot]

Going to merge this for now because the feature is added, the next thing is fixing the travis build which is a separate issue