Change sample sheet format to 1 row per cycle per channel

[RobJY]

sample sheet format: sample, cycle_number, channel_count, image_tiles

the marker sheet (markesrs.csv) will be input via a pipeline parameter

To Do:

• [x] change input_check.nf:create_fastq_channel():meta.id to sample_name + cycle
• [x] modify sample sheet schema for the new format (validation handled by nf-validation)
• [ ] image_tiles file(s) currently hard-coded in workflow. Need to use the file(s) in the sample sheet.
  • [x] working with one image, but will require change for multiple images
• [ ] add marker sheet pipeline parameter
• [ ] in validation function check:
  • [x] simple validation that required entries exist and that files have required suffix and that integers are actually integers
  • [ ] that channel_count in sample sheet matches the number of channels in the marker sheet
  • [ ] uniqueness of marker name in marker sheet
  • [ ] uniqueness of (cycle, channel) tuple in marker sheet
• [ ] add test(s)

[RobJY]

From our meeting today, changing format to 1 row per sample, so I'll create a new ticket for this. I'll start in my fork and then make a PR when I've got something done that might be useful.