Cleaned up and blocked-by-step GALA code ; many additional options#29

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JohnUrban wants to merge 34 commits intoganlab:masterfrom

JohnUrban:master

Commits on Oct 5, 2022

JohnUrban Fork first commit as described in johnurban_fork_changelog.txt
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JohnUrbanFork second commit - README.md updated.
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Commits on Oct 6, 2022

Third commit : resume and contine options, more messages during pipeline, more QC at each step.
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Fourth commit in JohnUrbanFork - updated README.md
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JohnUrbanFork commit : updated changelog and comp_generator
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Commits on Oct 7, 2022

Commits on Oct 9, 2022

JohnUrbanFork - gala script edited to better implement continue/dostep routines, especially regarding steps 8 and 9, and all the sub-steps therein, as well as keeping certain code (in a given step …
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Commits on Oct 10, 2022

Commits on Oct 11, 2022

Commits on Oct 12, 2022