tests: declare class:Collection / collection_type (epigenetics, data-fetching, chem, read-prep)

[jmchilton]

Schema regularization of workflow test files for epigenetics, data-fetching, computational chemistry, and read preprocessing. 10 workflow directories, all green in #1286's CI.

What this is

Split out of #1286, which bundled 55 workflow directories into one PR and could not complete CI (the PR test job caps at 4 chunks, so ~14 Galaxy test runs landed in each and chunk 0 was cancelled at GitHub's 6h job limit).

The change is purely mechanical schema regularization of workflow test files, in two patterns:

• class: Collection added to outputs that already carried element_tests: / elements: / collection-only attributes: — a declarative annotation of things already known to be collections.
• type: renamed to collection_type: on nested collection elements in job inputs.

No .ga workflow files and no expected test data are touched.

Why this one is expected green

Every workflow in this PR passed its planemo test run on the #1286 branch (CI run 29268785765), and all directories linted clean. This PR carries only those workflows, in a small enough set that CI can actually finish.

Workflows in #1286 that failed did so for pre-existing reasons unrelated to this schema change (a broken compleasm tool, tool revisions missing from the Toolshed, stale expected VCFs, flaky asserts). Those are held back in separate branches behind their underlying fixes.

Workflows

atacseq, average-bigwig-between-replicates, chipseq-pe, chipseq-sr, consensus-peaks, gromacs-dctmd, metadata-and-sequences-from-bioproject-ids, parallel-accession-download, sra-manifest-to-concatenated-fastqs, short-read-qc-trimming

[mvdbeek]

Attention: deployment skipped!

https://github.com/galaxyproject/iwc/actions/runs/29392033142