Phils update readme

[philsteinberg]

Description

Changed the README to contain the correct sSNV-caller and sCNA caller output and output directories. Updated details such as on node choices, modes, and completion of pipeline runs.

Checklist

• [x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• [x] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• [x] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [x] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
• [x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [x] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

[philsteinberg]

How do I remove the commits prior to Nov 15th? I branched off of main to create this branch, but I still have this trail of 5 changes because my local branch contains changes not on main. (I cannot push those because I cannot push to main.)

[lydiayliu]

Hmmm I think you can try to reverse your latest 2 commits on this local branch (copy out the changes somewhere), then you go to your local main branch and reverse the 5 commits, then you can add these 2 commits again to this branch

Alternatively, you can copy out the changes from these 2 commits, delete your local repo folder, clone it again, and commit again

But I don't think that's necessary. Your files changed look fine right now (with only updates to the CHANGELOG and README). Let me look through it and I think we are good to merge after the review. Don't worry about the commit history!