Improvements to chipseeker, contrast & input checks, docs

[slsevilla]

Changes

• adds the start for documenting samplesheet requirements, adds workflow page
• performs check on contrast manifest during input check
• increase resource allocation for chipseeker peakplot - temp patch until we can adjust cores to chipseeker internally
• organizes annotation directory into sub-folders; mirrors motif output
• fixes null being added to chipseeker annotate output files
• removes read_group from input_check
• increases resource allocation for deeptools

Issues

• contributes to overhaul documentation website #174
• feat need to run contrast manifest check earlier in the process; improve error message #181
• fixes ANNOTATE:CHIPSEEKER_PEAKPLOT failed due to memory allocation #183
• fixes organize ANNOTATE output into sub-folders by sample name #185
• fixes chipseeker_annotate is naming files with a "null" variable #186
• fixes remove 'read group' from input_check #191
• fixes Increase resources for deeptools #195

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
• [ ] Update docs if there are any API changes. on hold until before public release
  -[ ] If a new nextflow process is implemented, define the process container and stub.
• [] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[slsevilla]

submitted test job 20894186

[slsevilla]

Test failed, but not related to these changes. @kelly-sovacool when you run the test.config do you see a failure at chipseeker_annotate for one sample? I'm getting an error related to #193 but I think that's background noise because the results are not generating:

ls: cannot access 'SPT5_T0.gem/*.annotated.txt': No such file or directory
ls: cannot access 'SPT5_T0.gem/*.summary.txt': No such file or directory
ls: cannot access 'SPT5_T0.gem/*.genelist.txt': No such file or directory
ls: cannot access 'SPT5_T0.gem/*.annotation.Rds': No such file or directory
ls: cannot access 'SPT5_T0.gem/*.png': No such file or directory

[kelly-sovacool]

@slsevilla chipseeker annotate completes successfully for me with the test profile on main and iss-190.

[slsevilla]

alright well yay for this PR but not for the issue #193. I'll deal with that in the next PR.

[kelly-sovacool]

are boolean values supposed to be quoted in nextflow?

[kelly-sovacool]

we don't need contrasts in the config files now that main.nf checks for contrastsheet, right?

[kelly-sovacool]

should this be

Suggested change

	contrastsheet = params.contrastsheet ?: "/assets/contrast_test.ymls"
	contrastsheet = params.contrastsheet ?: "${projectDir}/assets/contrast_test.ymls"

to make sure it uses the project directory as root, instead of the root of the file system?

[kelly-sovacool]

Should/does this also address #196 since it includes a contrastsheet check in the main workflow file?

[kelly-sovacool]

Hey @kopardev you'll see I had left several comments and requested changes above, this wasn't ready to be merged. I'll just make the changes in a new PR, but I think it's generally better to resolve it in the same PR so everything is kept in one conversation thread and the main branch only has reviewed + working code.

[kopardev]

Hey @kopardev you'll see I had left several comments and requested changes above, this wasn't ready to be merged. I'll just make the changes in a new PR, but I think it's generally better to resolve it in the same PR so everything is kept in one conversation thread and the main branch only has reviewed + working code.

Also keep the PR as a draft... until ready to merge.

[kelly-sovacool]

Typically we keep PRs as drafts until ready for review, then we merge the PR after the reviewer approves it. I requested changes, so it wasn't approved. Unfortunately Sam didn't get around to making the changes I requested before she left.

I'll go ahead and make the changes. In the future please only merge a PR if it has been approved.