Pipeline output documentation

[drpatelh]

We will need to properly document/explain all of the outputs generated by the pipeline along with some nice plots and figures:
https://github.com/nf-core/atacseq/blob/dev/docs/output.md

[drpatelh]

This was initially added here #48

[ktrns]

Hi @drpatelh

I have made little changes here and there and will create a PR soon.

Questions that came up in usage.md:
Would it be possible to add a sentence to --amplicon_bed and --amplicon_fasta to say what it is needed for? Why is a bed file needed if we map the reads any way? Why is a fasta file needed if we assemble anyways? SOLVED - added some more description in the docs

Why are VarScan2 and iVar used for variant calling of reads against the reference genome, and Minimap2, seqwish, vg for variant calling of de-novo assemblies against the reference genome? Are the latter ones better suited for genome vs. genome? And why is specifically vg failing? Does --run_vg run specifically vg, or Minimap2 and seqwish as well? (I obviously don't know these tools yet and don't know about the concept of a variant graph yet)

Why is especially minia failing and hence not in the defaults for --assemblers? - SOLVED - minia added back in as default

Questions that came up in output.md:
Why are you using different trimming tools? fastp for general adapter trimming, iVar trim before variant calling, Cutadapt before de-novo assembly. SOLVED - Elaborated a bit more in each section to make the distinction clearer

Best
Katrin

[drpatelh]

Docs are looking nice now as of #103