PD-2660: Output files at cell level

[aawdeh]

Added new task called Summary_PerCellOutput to output the files as final outputs of the pipeline at a cell level: all_reads_3C_contacts, name_sorted_bam, unique_reads_cgn_extraction_allc, unique_reads_cgn_extraction_allc_extract, unique_reads_cgn_extraction_tbi and unique_reads_cgn_extraction_tbi_extract

Removed hisat3n_dna.all_reads.dedup_contact and chromatin_contact_stats as requested by Ecker lab

---

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

• [ ] Did you add inputs, outputs, or tasks to a workflow?
• [ ] Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• [ ] If you made a changelog update, did you update the pipeline version number?

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed