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Adding STAR aligner metrics and snm3c diagram #1394

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merged 6 commits into from
Oct 18, 2024
Merged

Adding STAR aligner metrics and snm3c diagram #1394

merged 6 commits into from
Oct 18, 2024

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ekiernan
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This PR adds documentation changes, specifically:

  1. The addition of a new document describing the STARsolo alignment metrics TAR.
  2. A diagram for the snm3C workflow.

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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

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🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

aawdeh
aawdeh reviewed Oct 18, 2024
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website/docs/Pipelines/snM3C/snm3C_diagram.png Outdated
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Should we make the unique mapped reads BAM and Aligned BAMs the same color

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One is intermediate and one is final output. I will add a key to the diagram.

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Thanks!

@ekiernan @nikellepetrillo
Update website/docs/Pipelines/Optimus_Pipeline/starsolo-metrics.md
315a6ba 
Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>
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@ekiernan @nikellepetrillo
Update website/docs/Pipelines/Optimus_Pipeline/starsolo-metrics.md
3a833f2 
Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>
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🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@github-actions GitHub Actions
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Remember to squash merge!

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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

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🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

nikellepetrillo
nikellepetrillo reviewed Oct 18, 2024
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website/docs/Pipelines/Optimus_Pipeline/starsolo-metrics.md Outdated
| intronic | Number of reads mapping to annotated introns;these are only calculated for --soloFeatures GeneFull_Ex50pAS and/or GeneFull_ExonOverIntron. |
| exonicAS | Number of reads mapping antisense to annotated exons. |
| intronicAS | Number of reads mapping antisense to annotated introns; these are only calculated for --soloFeatures GeneFull_Ex50pAS. |
| mito | for the number of read mapping on mitochondrial genome. |
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Suggested change
| mito | for the number of read mapping on mitochondrial genome. |
| mito | Number of reads mapping to the mitochondrial genome. |

nikellepetrillo
nikellepetrillo approved these changes Oct 18, 2024
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super tiny suggestions. thank you!

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Remember to squash merge!

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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@github-actions GitHub Actions
Copy link

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

aawdeh
aawdeh approved these changes Oct 18, 2024
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LGTM!

@ekiernan ekiernan merged commit 23d2cbc into develop Oct 18, 2024
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@ekiernan ekiernan deleted the lk-adding-doc-updates-20241018 branch October 18, 2024 19:32
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@aawdeh aawdeh aawdeh approved these changes

@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

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@ekiernan @aawdeh @nikellepetrillo