fix(sra): improve layout extraction from NCBI db

[mkatsanto]

Description

The issue is described in #166 . The solution applied is that only for samples that either the PAIRED or SINGLE library layouts, the samples will pass through the workflow, otherwise the samples are silently dropped. As for the recovery of the layout in the get_layout rule, there is an improvement in the syntax as there was no need for the csv2xml that was causing the issue in the first place, as there is already an option of -mode xml in the efetch command that then allows direct extraction of the layout feature.

Fixes #166

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)

Conventional Commits guidelines

• I made sure the PR title follows the
  https://www.conventionalcommits.org/en/v1.0.0/

Changes to workflow inputs (sample table and/or configs)

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • more fields/properties are required
  • existing ones are dropped entirely
• minor (add feat: in the beginning of the PR title)
  • optional fields/properties are added
  • required ones are made optional

Changes to workflow outputs

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • changes lead to removal/change of existing outputs (format or location)
• minor (add feat: in the beginning of the PR title)
  • additional outputs are generated
  • content (but not format or location) of existing outputs changes

Everything else: patch
(add any other conventional commit in the beginning of the PR title)

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• New and existing tests pass locally with my changes

[uniqueg]

It looks and sounds good to me, but I find it a bit hard to review it. How extensively have you tested it on real data?

[mkatsanto]

I tried with some non-existent names and then with the examples failing in issue #166. I could try a few more random ones.