Bin dir, CI build fixes

See merge request !8

Script cleanup from @mhalache

See merge request !5

NextFlow variant calling

See merge request !4

# Conflicts:
#   README.md

Doc updates, updating format of sample sheets. Adding nextflow.config. Adding main.nf entrypoint, moving param declarations there. Making most input parameters their own Channels.

Adding parse_peddy_output check, simplifying process inputs/outputs. Outputting BCBio outputs properly, fixing outputs at end - cp-RL and mode: move. Pulling changes to trio_whole_exome_parse_peddy_ped_csv.pl from ultra2 branch

Adding process labels for resource managers. Fixing fastq merging, BCBio. Adding recognition for other input run formats.

NextFlow

See merge request !1