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Platform tutorial: nf-core/rnaseq full #131

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75b3332
First commit
llewellyn-sl Jul 22, 2024
64dbdf3
RNA-seq guide one-pager draft
llewellyn-sl Jul 23, 2024
2e5d9cc
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Jul 23, 2024
c94f373
Small fixes
llewellyn-sl Jul 23, 2024
ce85802
FOrmatting fixes for preview readability
llewellyn-sl Jul 23, 2024
fe143ce
Update rnaseq.mdx
llewellyn-sl Jul 24, 2024
14b301b
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Sep 10, 2024
5c9d9a2
Update wave_repo
llewellyn-sl Sep 10, 2024
33e432a
Update rnaseq.mdx
llewellyn-sl Sep 11, 2024
9cc3787
DS initial commit
llewellyn-sl Sep 16, 2024
ab4d8df
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Sep 17, 2024
780018f
Merge branch 'rnaseq-full-guide' of https://github.com/seqeralabs/doc…
llewellyn-sl Sep 17, 2024
b2a665b
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Sep 20, 2024
0e75d4c
Update rnaseq.mdx
llewellyn-sl Sep 20, 2024
6f27caf
Merge branch 'rnaseq-full-guide' of https://github.com/seqeralabs/doc…
llewellyn-sl Sep 20, 2024
191fea9
Strip out Azure and GCP, add RStudio config
llewellyn-sl Sep 20, 2024
ae4daf7
Add Fusion, collapse monitoring and optimization section
llewellyn-sl Sep 23, 2024
9a71991
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Sep 27, 2024
e086d5a
Add compute benchmarks
llewellyn-sl Sep 27, 2024
8cd029e
Split studio script, improve instructions
llewellyn-sl Sep 30, 2024
0f44680
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Sep 30, 2024
e27b16f
Update rnaseq.mdx
llewellyn-sl Sep 30, 2024
990b307
Merge branch 'rnaseq-full-guide' of https://github.com/seqeralabs/doc…
llewellyn-sl Sep 30, 2024
c17c0a1
Add GIFs, add run cost comparison
llewellyn-sl Oct 1, 2024
813f9ef
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Oct 1, 2024
25b277b
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 2, 2024
1cc59b9
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 2, 2024
089633b
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 2, 2024
b4b905b
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 2, 2024
1acf651
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 2, 2024
419368a
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
bb13520
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
ea96fea
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
deec33d
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
edda033
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
9f25f3a
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
c005006
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
6a9f2a3
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
ef67df8
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
c66fb03
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
bbc837d
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
1b0aaad
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 4, 2024
43ad7db
Merge branch 'master' into rnaseq-full-guide
llewellyn-sl Oct 4, 2024
4140949
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 6, 2024
c43d6ad
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 6, 2024
c82d347
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 6, 2024
0b2ec56
Update platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx
llewellyn-sl Oct 6, 2024
817d844
Add subway map, code review suggestions
llewellyn-sl Oct 6, 2024
143eb56
Merge branch 'rnaseq-full-guide' of https://github.com/seqeralabs/doc…
llewellyn-sl Oct 6, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ Platform offers two methods to import pipelines to your workspace Launchpad —

![Seqera Pipelines overview](assets/seqera-pipelines-overview.gif)

To import the `nf-core/rnaseq` pipeline:
To import the `nf-core-rnaseq` pipeline:

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Suggested change
To import the `nf-core-rnaseq` pipeline:
To import the `nf-core/rnaseq` pipeline:

The gif above shows nf-core/rnaseq as the title, is there a reason you wanted to change it to nf-core-rnaseq?

1. Select **Launch** next to the pipeline name in the list. In the **Add pipeline** tab, select **Cloud** or **Enterprise** depending on your Platform account type, then provide the information needed for Seqera Pipelines to access your Platform instance:
- **Seqera Cloud**: Paste your Platform **Access token** and select **Next**.
- **Seqera Enterprise**: Specify the **Seqera Platform URL** (hostname) and **Base API URL** for your Enterprise instance, then paste your Platform **Access token** and select **Next**.
Expand All @@ -37,7 +37,7 @@ To launch pipelines directly with CLI tools, select the **Launch Pipeline** tab
![Launch Seqera Pipeline](assets/seqera-pipelines-launch-cli.png)
:::

### Add nf-core/rnaseq from the Launchpad
### Add nf-core/rnaseq manually

![Add nf-core/rnaseq pipeline](assets/sp-cloud-add-rnaseq.gif)

Expand Down
752 changes: 752 additions & 0 deletions platform_versioned_docs/version-23.4/getting-started/rnaseq.mdx

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11 changes: 2 additions & 9 deletions platform_versioned_sidebars/version-23.4-sidebars.json
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
"label": "Tutorials",
"collapsed": true,
"items": [
"getting-started/quickstart-demo/comm-showcase"
"getting-started/quickstart-demo/comm-showcase",
"getting-started/rnaseq"
]
},
{
Expand Down Expand Up @@ -84,7 +85,6 @@
"type": "category",
"label": "Data",
"items": [
"getting-started/quickstart-demo/add-data",
"data/data-explorer",
"data/datasets"
]
Expand All @@ -93,7 +93,6 @@
"type": "category",
"label": "Pipelines",
"items": [
"getting-started/quickstart-demo/add-pipelines",
"pipeline-schema/overview",
"launch/launchpad",
"labels/overview",
Expand All @@ -117,7 +116,6 @@
"type": "category",
"label": "Administration",
"items": [
"getting-started/workspace-setup",
"administration/overview",
"orgs-and-teams/organizations",
"orgs-and-teams/workspace-management",
Expand Down Expand Up @@ -186,11 +184,6 @@
"label": "Developer tools",
"collapsed": true,
"items": [
{
"type": "doc",
"id": "getting-started/quickstart-demo/automation",
"label": "Overview"
},
"api/overview",
{
"type": "category",
Expand Down
8 changes: 0 additions & 8 deletions platform_versioned_sidebars/version-24.1-sidebars.json
Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,6 @@
"type": "category",
"label": "Data",
"items": [
"getting-started/quickstart-demo/add-data",
"data/data-explorer",
"data/datasets"
]
Expand All @@ -94,7 +93,6 @@
"type": "category",
"label": "Pipelines",
"items": [
"getting-started/quickstart-demo/add-pipelines",
"pipeline-schema/overview",
"launch/launchpad",
"labels/overview",
Expand All @@ -119,7 +117,6 @@
"type": "category",
"label": "Administration",
"items": [
"getting-started/workspace-setup",
"administration/overview",
"orgs-and-teams/organizations",
"orgs-and-teams/workspace-management",
Expand Down Expand Up @@ -190,11 +187,6 @@
"label": "Developer tools",
"collapsed": true,
"items": [
{
"type": "doc",
"id": "getting-started/quickstart-demo/automation",
"label": "Overview"
},
"api/overview",
{
"type": "category",
Expand Down
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