Develop

.github/workflows/bbknn_scenic.yml

@@ -0,0 +1,36 @@
+name: bbknn_scenic
+
+on: 
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        submodules: true
+    - name: Install Nextflow
+      run: |
+        export NXF_VER='19.12.0-edge'
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+    - name: Get sample data
+      run: |
+        mkdir testdata
+        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz
+        tar xvf sample_data_small.tar.gz
+        cp -r sample_data testdata/sample1
+        mv sample_data testdata/sample2
+    - name: Run bbknn_scenic test
+      run: |
+        nextflow run ${GITHUB_WORKSPACE} -profile bbknn_scenic,test__bbknn_scenic,docker -entry bbknn_scenic -ansi-log false
+        cat .nextflow.log
+

.github/workflows/mnncorrect.yml

@@ -25,8 +25,8 @@ jobs:
     - name: Get sample data
       run: |
         mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
-        tar xvf sample_data_tiny.tar.gz
+        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz
+        tar xvf sample_data.tar.gz
         cp -r sample_data testdata/sample1
         mv sample_data testdata/sample2
     - name: Run single_sample test

README.rst

@@ -15,8 +15,48 @@ VSN-Pipelines
     :target: https://gitter.im/vib-singlecell-nf/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge
     :alt: Gitter
 
+|single_sample| |single_sample_scenic| |scenic| |scenic_multiruns| |single_sample_scenic_multiruns| |bbknn| |bbknn_scenic| |harmony| |mnncorrect|
+
+.. |single_sample| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#single-sample-single-sample
+    :alt: Single-sample Pipeline
+
+.. |single_sample_scenic| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample_scenic/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#single-sample-scenic-single-sample-scenic
+    :alt: Single-sample SCENIC Pipeline
+
+.. |scenic| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/scenic/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-scenic
+    :alt: SCENIC Pipeline
+
+.. |scenic_multiruns| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/scenic_multiruns/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-multiruns-scenic-multiruns-single-sample-scenic-multiruns
+    :alt: SCENIC Multi-runs Pipeline
+
+.. |single_sample_scenic_multiruns| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample_scenic_multiruns/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-multiruns-scenic-multiruns-single-sample-scenic-multiruns
+    :alt: Single-sample SCENIC Multi-runs Pipeline
+
+.. |bbknn| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/bbknn/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#bbknn-bbknn
+    :alt: BBKNN Pipeline
+
+.. |bbknn_scenic| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/bbknn_scenic/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#bbknn-scenic
+    :alt: BBKNN SCENIC Pipeline
+
+.. |harmony| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/harmony/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#harmony-harmony
+    :alt: Harmony Pipeline
+
+.. |mnncorrect| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/mnncorrect/badge.svg
+    :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#mnncorrect-mnncorrect
+    :alt: MNN-correct Pipeline
+
 A repository of pipelines for single-cell data in Nextflow DSL2.
 
+Do you want a quick tour of the VSN pipelines ? Please read `Quick Start <https://vsn-pipelines.readthedocs.io/en/latest/getting-started.html#quick-start>`_.
+
 Full documentation available on `Read the Docs <https://vsn-pipelines.readthedocs.io/en/latest/>`_
 
 This main repo contains multiple workflows for analyzing single cell transcriptomics data, and depends on a number of tools, which are organized into submodules within the VIB-Singlecell-NF_ organization.