Change samplesheet parsing

[KateSakharova]

Description of feature

We add fields from samplesheet like

    assembly_fasta = ch_samplesheet
        .map { row ->
            def meta = [
                id: row[0].id,
                single_end: row[3] ? false : true,
                coverage: row[4] ?: null,
                run_accession: row[5],
                assembler: row[6],
                assembler_version: row[7]
            ]
            [meta, file(row[1])]
        }

which requires correct order of columns.

Instead we can add it to meta in schema like we do for sample

            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample must be provided and cannot contain spaces",
                "meta": ["id"]
            },

It is applicable to all three workflows.
After fixing it we need to change README (James had a comment about it)

fix docs/usage.md in

> [!IMPORTANT]
> **Samplesheet column requirements**: All columns shown in the example above must be present in your samplesheet, even if some values are empty. Columns must be in exactly the same order as shown.