Write Documentation about ampliseq HOT 3 CLOSED

usage.md is updated, but:

The typical command for running the pipeline is as follows:
nextflow run nf-core/rrna-ampliseq --reads 'data' -profile standard,docker

still needs to be adjusted! Somehow havent seen that one!

edit: also table of contents needs adjustments... still imperfect

edit2: todo list for each document:

• usage.md : table of contents, "typical command", polishing, mention standard database SILVA v132 99% derep
• troubleshooting.md : complete rewrite
• output.md : add explanation for tons of output
• installation.md : seems fine
• README.md : remove link to "Reference genomes", add general short overview what pipeline does + central methods
• configuration/reference_genomes.md : delete
• configuration/adding_your_own.md : seems fine

edit3: added more todo's

from ampliseq.

Modified:

• docs/usage.md: table of contents
• docs/README.md: remove link to docs/configuration/reference_genomes.md
• README.md: add general short overview what pipeline does + central methods
• docs/configuration/reference_genomes.md: deleted
• docs/troubleshooting.md : added meaningful guidelines to troubleshooting

Still to do:

• docs/output.md : add explanation for tons of output

edit: added changes to docs/troubleshooting.md

from ampliseq.

Done, might need still polishing or small adjustments though.

from ampliseq.