🎨 Simplify use case by moving to nf-core/scrnaseq (#42)

* 🎨 Simplify use case Signed-off-by: zethson <[email protected]> * 🎨 Fix use case Signed-off-by: zethson <[email protected]> * 🎨 Fix use case Signed-off-by: zethson <[email protected]> * 🎨 Fix use case Signed-off-by: zethson <[email protected]> * 🎨 Debug Signed-off-by: zethson <[email protected]> * 🎨 Properly install lamindb Signed-off-by: zethson <[email protected]> * 🎨 Properly install lamindb Signed-off-by: zethson <[email protected]> * 🎨 Proper script again Signed-off-by: zethson <[email protected]> * 🎨 Refactoring Signed-off-by: zethson <[email protected]> * 🎨 Refactoring Signed-off-by: zethson <[email protected]> * 🎨 Split into two parts Signed-off-by: zethson <[email protected]> * 🎨 Improve wording Signed-off-by: zethson <[email protected]> * 🎨 Not str Signed-off-by: zethson <[email protected]> * 🎨 Try linage Signed-off-by: zethson <[email protected]> * 🎨 Try linage Signed-off-by: zethson <[email protected]> * 🎨 Try lineage Signed-off-by: zethson <[email protected]> * 🎨 Try lineage Signed-off-by: zethson <[email protected]> * 🎨 Show cell again Signed-off-by: zethson <[email protected]> * 🎨 Remove tests lineage Signed-off-by: zethson <[email protected]> * 🎨 Display code Signed-off-by: zethson <[email protected]> * ✨ Move to nf-core/scrnaseq Signed-off-by: zethson <[email protected]> * 🎨 Add jupyter ot lamindb deps Signed-off-by: zethson <[email protected]> * 🎨 Add jupyter ot lamindb deps Signed-off-by: zethson <[email protected]> * 🎨 Debug Signed-off-by: zethson <[email protected]> * 🎨 Debug Signed-off-by: zethson <[email protected]> * 🎨 Tree Signed-off-by: zethson <[email protected]> * 🎨 Fix output dir Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Functionize Signed-off-by: zethson <[email protected]> * 🎨 Polishing and fix script display Signed-off-by: zethson <[email protected]> * 🎨 Less scary script Signed-off-by: zethson <[email protected]> * 🎨 Ruff Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Polish Signed-off-by: zethson <[email protected]> * 🎨 Hide-cell Signed-off-by: zethson <[email protected]> * 💄 Polish notebook * 💚 Add a comment to the script * 🎨 Remove ln.track() from registration script * 💚 Fix by no longer relying on global run context * 🎨 Fix script Signed-off-by: zethson <[email protected]> * 🎨 Add screenshot Signed-off-by: zethson <[email protected]> * 🎨 Improve workflow Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Alex Wolf <[email protected]>
laminlabs · Oct 3, 2024 · a7bbf2d · a7bbf2d
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commit a7bbf2d
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Showing 12 changed files with 376 additions and 20,793 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,32 +10,32 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_EVENT_NAME: ${{ github.event_name }}
       NXF_ANSI_LOG: false
     strategy:
       fail-fast: false
-    timeout-minutes: 50
+    timeout-minutes: 30
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           repository: laminlabs/lndocs
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml"
-      - uses: nf-core/setup-nextflow@v1
+          python-version: "3.11"
+
+      - uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-stable"
+
       - uses: actions/cache@v3
         with:
           path: ~/.cache/pre-commit

diff --git a/.gitignore b/.gitignore
@@ -112,12 +112,9 @@ _docs_tmp*
 # Nextflow
 .nextflow*
 work
-fetchngs-results
-nextflow_rna_seq
-rna-seq-results
 multiqc_report.html
-differentialabundance-results
 test-datasets
-nextflow-mcmicro
-exemplar-001
-exemplar-001-mcmicro-execution_report.html
+test-nextflow
+scrnaseq_input
+scrnaseq_output
+test.ipynb
diff --git a/docs/index.md b/docs/index.md
@@ -7,6 +7,6 @@
 :maxdepth: 1
 :hidden:
 
-mcmicro
+nf_core_scrnaseq
 changelog
 ```
diff --git a/docs/mcmicro.ipynb b/docs/mcmicro.ipynb
diff --git a/docs/mcmicro.py b/docs/mcmicro.py