Update CWL paths

[vedran-kasalica]

This pull request updates the cwlVersion in several CWL tool files from v1.0 to v1.2 and modifies a configuration file to update a URL path to the correct one.

The changes ensure that the CWL version used aligns with our guidelines and that the template domain is well annotated.

[eladrion]

@vedran-kasalica If I see that correctly, you bump the CWL version to 1.2 here, which is done for most of the files in PR #87, too. Only one change is different, i.e. in domains/template-domain/config.json, the tool_annotations_path is set to https://raw.githubusercontent.com/Workflomics/containers/main/domains/template-domain/tools.json. In PR #87, this path is already modified to https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/YOUR-BRANCH-NAME/domains/proteomics_new/tools.json. This change seems to be obsolete. I will mark the obsolete changes and the ones that could be ported to #87.

[eladrion]

Already set in PR #87, file cwl-tools/comet/comet.cwl

[eladrion]

Not yet updated in #87

[eladrion]

Already set in PR #87, file cwl-tools/msfragger/msfragger.cwl

[eladrion]

Already set in PR #87, file cwl-tools/ms_amada/ms_amada.cwl

[eladrion]

Already set in main

[eladrion]

Already set in main

[eladrion]

Not yet updated in #87, nor in main

[eladrion]

Already set in PR #87, file cwl-tools/xtandem/xtandem.cwl

[eladrion]

Already set in PR #87, file cwl-tools/gprofiler/gprofiler.cwl

[eladrion]

Not yet updated in PR #87, nor in main

[eladrion]

Already set in PR #87, file cwl-tools/protCml2IdList/protCml2IdList.cwl

[eladrion]

Not yet updated #87, nor in main

[eladrion]

Not yet updated #87, nor in main

[eladrion]

Obsolete by #87