Add nf-core-tools, and three remainder deps (#34466)

* nextflow recipe: added latest stable version

* tower-cli recipe: added latest release

* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli

* recipes nf-tower-agent and nf-tower-cli: small fix

* nf-core-tools recipe: added most py- dependencies

* nf-core-tools: recipe without galaxy-tool-util (for testing)

* fixed typos in py-yacman recipe

* fixed typos in py-pytest-workflow recipe

* fixed typo in nf-core-tools recipe

* fixed typos in py-yacman recipe

* fixes in recipes for py-questionary and py-url-normalize

* fixes to py-yacman recipe

* style fixes to py- packages that are dependencies to nf-core-tools

* fix in py-requests-cache recipe

* added missing dep in py-requests-cache recipe

* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper

* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util

* nf-core-tools: new version with extra dependency

* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps

* nextflow and nf-core-tools packages: added my self as maintainer

* style fixes

* style fix for nf-core-tools recipe

* added license to py-logmuse recipe

* audit fixes

* style fix after audit fix

* py-galaxy-tool-util: added deps 1st bunch

* audit/style fixes, including adding missing dep package

* more audit/style fixes

* more more audit/style fixes

* moooore audit fixes

* py-galaxy-tool-util: dependencies 2nd chunk

* silly audit fix

* py-galaxy-util deps: 3rd bunch - first 20 done

* fixes

* style fix

* py-galaxy-tool-util: 4th bunch of deps

* stashing dep recipe backbones for py-galaxy-tool-util

* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util

* nf-core-tools: adding also py-galaxy-util, as wheel

* fix

* nextflow: added latest bugfix version

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* nf-core-tools pr: 1st bunch of review edits

* nf-core-tools: 2nd bunch of review edits

* adding back tower-agent and tower-cli as deprecated

* nf-core-tools: 3rd bunch of review edits

* small style fix

* prepping py-galaxy-tool-util for further work

* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar

* audit fixes

* updates to py-galaxy-tool-util and its deps, still 2 to work on

* one style fix

* updated recipe for py-galaxy-util

* updated recipe for py-pulsar-galaxy-lib

* typo fix

* shasum fixes

* updated py-sqlalchemy from develop

* added newest versions (today) for nf-tower-agent and nf-tower-cli

* Update var/spack/repos/builtin/packages/py-requests-cache/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-requests-cache/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* adding 2nd bunch of nf-core deps from update/nextflow-tools

* adding 3rd bunch of nf-core deps from update/nextflow-tools

* 4th chunk of nf-core deps from update/nextflow-tools

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pebble/package.py

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* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-gunicorn/package.py

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* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-parsley/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-gxformat2: added comment

* py-lagom: now using github tarballs

* fix for py-lagom

* adding missing deps to py-fastapi-utils

* another fix to py-lagom

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-lagom/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-supervisor/package.py

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* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fixes from PR review

* adding missing deps, from PR review

* py-galaxy2cwl from github tarball, as per PR review

* fix to py-tuswsgi, as per PR review

* nf-tools: edits from PR review

* adding 3x more galaxy deps

* fix

* fixing circular dep of py-poetry-plugin-export with py-poetry

* added newest nf-core-tools version

* Update var/spack/repos/builtin/packages/py-galaxy-util/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fix in py-poetry-plugin-export

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

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