Quasispecies Reconstruction Benchmark

[kpj]

This PR is the home of the quasispecies reconstruction benchmark workflow. Eventually, it will make its way to master.

[github-actions[bot]]

MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Elapsed time
✅ BASH	shellcheck	6		0	0.16s
✅ MARKDOWN	markdownlint	6	6	0	0.83s
✅ PYTHON	black	19	1	0	1.4s
✅ SNAKEMAKE	snakefmt	19	3	0	6.59s

See errors details in artifact MegaLinter reports on CI Job page

[github-actions[bot]]

MegaLinter status: ❌ ERROR

Descriptor	Linter	Files	Fixed	Errors	Elapsed time
✅ BASH	shellcheck	10		0	0.28s
✅ DOCKERFILE	hadolint	1		0	0.57s
✅ JUPYTER	jupyfmt	3	3	0	3.43s
❌ MARKDOWN	markdownlint	10	9	1	1.09s
✅ PERL	perlcritic	1		0	1.1s
✅ PYTHON	black	61	38	0	6.95s
✅ SNAKEMAKE	snakefmt	24	2	0	13.73s

See errors details in artifact MegaLinter reports on CI Job page

[DrYak]

@kpj : If I am not mistaken, most of the benchmark was merged together with the big merge for @LaraFuhrmann 's workshop.

By now the benchmark is already in V-pipe

And this old PR is deprecated. Am I correctly presuming?

[kpj]

Not sure what was merged in the workshop PR. So I don't know if this PR is deprecated.

[LaraFuhrmann]

Seems like it is in the master. I was not aware of that.

[DrYak]

Okay got-it:

fa3b74e5533cb24cc58d572119d7b2c1d0a6feb9 from this branch is the last one that is merged into master (as-is, no rebase, just merge).

from 230b90c81171ca1f94fbfca93fb0b386e6f819bc onward to 7eb83a434e086bb8ea9f15f84ed9a77b928b504e is not yet in master.

As the feature-benchmark as merged as-is (no rebase), adding them on top shouldn't be that difficult. (Probably not too many conflict except for linting-related stuff).

Will start merging in as soon as v2.99.3 is out now.

[DrYak]

I managed to merge. Indeed, most of discepencies were snakefmt linting, and the switching to runtime resource by snakemake.

Now in rubicon as of e844fa6d1c505cd8db03c2831d8df30ad85df979