Patch fix for dev eval modules

• fixes three outdated conda env statements in the dev/eval modules
• updates citation info

Main assembly (CLR/HiFi) plus dev evaluation modules

• production release of main assembly pipeline (CLR or HiFi, plus Strand-seq)
• only experimental support for ONT
• requires long reads and Strand-seq
• dev status: evaluation modules (some require Illumina short reads as additional input)
• support for CLR is likely to be reduced or dropped in future releases
• processing of HiFi reads is no longer state-of-the-art (see other dev branches)

Dev release of pipeline for submission

Release corresponding to state of the code used for current submission. The follow-up of this release (after revision) will be the first production release

Release for revision stage of pipeline

Release of pipeline code corresponding to the revision stage of the manuscript (as submitted).
This release includes a substantial amount of documentation, and is being deployed at other research centers.

v0.0.2dev

Release from dev branch roughly corresponding to the state at the time of initial submission.
Pipeline is - at least in principle - start-to-finish including download of input data. Potential checkpoint issues not resolved, but being circumvented via generation of lots (?) of fofn-style files for the various merge operations.
This version does not yet include support for containerized tools.

First start-to-finish pipeline version

Limitations:

1. Requires manual download/linking of some input data (mostly, HGSVC PacBio data)
2. Probably a faulty checkpoint evaluation by Snakemake usually interferes with a "one-touch" pipeline run
3. Evaluation of results essentially limited to Quast-LG and some basic statistics about the input data
4. Haploid assembly works only genome-wide, i.e., not yet on a "per-chromosome, per-haplotype" basis