Merge pull request #293 from vib-singlecell-nf/develop

Develop for v0.25.0
vib-singlecell-nf · Jan 26, 2021 · 721c42f · 721c42f
2 parents 91e5724 + 71aac25
commit 721c42f
Show file tree

Hide file tree

Showing 187 changed files with 848 additions and 747 deletions.
diff --git a/.github/workflows/bbknn.yml b/.github/workflows/bbknn.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         mkdir testdata

diff --git a/.github/workflows/bbknn_scenic.yml b/.github/workflows/bbknn_scenic.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         mkdir testdata

diff --git a/.github/workflows/decontx.yml b/.github/workflows/decontx.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz

diff --git a/.github/workflows/harmony.yml b/.github/workflows/harmony.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         mkdir testdata

diff --git a/.github/workflows/mnncorrect.yml b/.github/workflows/mnncorrect.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         mkdir testdata

diff --git a/.github/workflows/scenic.yml b/.github/workflows/scenic.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Run scenic test
       run: |
         nextflow run ${GITHUB_WORKSPACE} -profile scenic,test__scenic,test__compute_resources,docker -entry scenic -ansi-log false

diff --git a/.github/workflows/scenic_multiruns.yml b/.github/workflows/scenic_multiruns.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Run scenic test
       run: |
         nextflow run ${GITHUB_WORKSPACE} -profile scenic_multiruns,test__scenic_multiruns,test__compute_resources,docker -entry scenic -ansi-log false

diff --git a/.github/workflows/single_sample.yml b/.github/workflows/single_sample.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz

diff --git a/.github/workflows/single_sample_decontx.yml b/.github/workflows/single_sample_decontx.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz

diff --git a/.github/workflows/single_sample_decontx_scrublet.yml b/.github/workflows/single_sample_decontx_scrublet.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz

diff --git a/.github/workflows/single_sample_param_exploration.yml b/.github/workflows/single_sample_param_exploration.yml
@@ -0,0 +1,34 @@
+name: single_sample_param_exploration
+
+on: 
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Nextflow
+      run: |
+        export NXF_VER='20.10.0'
+        wget -qO- get.nextflow.io | bash
+        sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
+    - name: Get sample data
+      run: |
+        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
+        tar xzvf sample_data_tiny.tar.gz
+    - name: Run single_sample_param_exploration test
+      run: |
+        nextflow run ${GITHUB_WORKSPACE} -profile single_sample,test__single_sample_param_exploration,test__compute_resources,docker -entry single_sample -ansi-log false
+        cat .nextflow.log
+
diff --git a/.github/workflows/single_sample_scenic.yml b/.github/workflows/single_sample_scenic.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz

diff --git a/.github/workflows/single_sample_scenic_multiruns.yml b/.github/workflows/single_sample_scenic_multiruns.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz

diff --git a/.github/workflows/single_sample_scrublet.yml b/.github/workflows/single_sample_scrublet.yml
@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   build:
@@ -15,13 +17,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Install Nextflow
       run: |
-        export NXF_VER='20.04.1'
+        export NXF_VER='20.10.0'
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
+        echo 0 | sudo tee /proc/sys/fs/protected_hardlinks
     - name: Get sample data
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz