Merge pull request #358 from vib-singlecell-nf/develop

Develop for v0.27.0
vib-singlecell-nf · Dec 3, 2021 · 96cff8e · 96cff8e
2 parents 962111a + 2f9e645
commit 96cff8e
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -38,8 +38,8 @@ If applicable, add screenshots to help explain your problem.
 
 **Please complete the following information:**
  - OS: [e.g. Ubuntu]
- - Nextflow Version: [e.g. 20.10.0]
- - vsn-pipelines Version: [e.g. 0.26.1]
+ - Nextflow Version: [e.g. 21.04.3]
+ - vsn-pipelines Version: [e.g. 0.27.0]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/workflows/bbknn.yml b/.github/workflows/bbknn.yml
@@ -1,6 +1,6 @@
 name: bbknn
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,25 +12,23 @@ on:
 
 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/
-    - name: Get sample data
-      run: |
-        mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
-        tar xzvf sample_data_tiny.tar.gz
-        cp -r sample_data testdata/sample1
-        mv sample_data testdata/sample2
-    - name: Run single_sample test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile bbknn,test__bbknn,test__compute_resources,docker -entry bbknn -ansi-log false
-        cat .nextflow.log
-
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          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_tiny.tar.gz
+          tar xzvf sample_data_tiny.tar.gz
+          cp -r sample_data testdata/sample1
+          mv sample_data testdata/sample2
+      - name: Run single_sample test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile bbknn,test__bbknn,test__compute_resources,docker -entry bbknn -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/bbknn_scenic.yml b/.github/workflows/bbknn_scenic.yml
@@ -1,6 +1,6 @@
 name: bbknn_scenic
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,25 +12,23 @@ on:
 
 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/
-    - name: Get sample data
-      run: |
-        mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz
-        tar xzvf 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,test__compute_resources,docker -entry bbknn_scenic -ansi-log false
-        cat .nextflow.log
-
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          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 xzvf 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,test__compute_resources,docker -entry bbknn_scenic -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/cell_annotate_filter.yml b/.github/workflows/cell_annotate_filter.yml
@@ -1,6 +1,6 @@
 name: cell_annotate_filter
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,22 +12,21 @@ on:
 
 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/
-    - name: Get sample data & dummy annotation
-      run: |
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
-        tar xzvf sample_data_tiny.tar.gz
-        wget https://raw.githubusercontent.com/vib-singlecell-nf/vsn-pipelines/develop/data/sample_data_tiny/sample_data_tiny_dummy_annotation.tsv.gz
-    - name: Run cell_annotate_filter test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile utils_cell_annotate_filter,test__cell_annotate_filter,test__compute_resources,docker -entry cell_annotate_filter -ansi-log false
-        cat .nextflow.log
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Get sample data & dummy annotation
+        run: |
+          wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
+          tar xzvf sample_data_tiny.tar.gz
+          wget https://raw.githubusercontent.com/vib-singlecell-nf/vsn-pipelines/develop/data/sample_data_tiny/sample_data_tiny_dummy_annotation.tsv.gz
+      - name: Run cell_annotate_filter test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile utils_cell_annotate_filter,test__cell_annotate_filter,test__compute_resources,docker -entry cell_annotate_filter -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/decontx.yml b/.github/workflows/decontx.yml
@@ -1,6 +1,6 @@
 name: decontx
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,21 +12,20 @@ on:
 
 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/
-    - name: Get sample data
-      run: |
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz
-        tar xzvf sample_data.tar.gz
-    - name: Run decontx test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile decontx,test__decontx,test__compute_resources,docker -entry decontx -ansi-log false
-        cat .nextflow.log
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Get sample data
+        run: |
+          wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz
+          tar xzvf sample_data.tar.gz
+      - name: Run decontx test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile decontx,test__decontx,test__compute_resources,docker -entry decontx -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/harmony.yml b/.github/workflows/harmony.yml
@@ -1,6 +1,6 @@
 name: harmony
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,24 +12,23 @@ on:
 
 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/
-    - name: Get sample data
-      run: |
-        mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz
-        tar xzvf sample_data_tiny.tar.gz
-        cp -r sample_data testdata/sample1
-        mv sample_data testdata/sample2
-    - name: Run single_sample test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile harmony,test__harmony,test__compute_resources,docker -entry harmony -ansi-log false
-        cat .nextflow.log
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          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_tiny.tar.gz
+          tar xzvf sample_data_tiny.tar.gz
+          cp -r sample_data testdata/sample1
+          mv sample_data testdata/sample2
+      - name: Run single_sample test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile harmony,test__harmony,test__compute_resources,docker -entry harmony -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/harmony_scenic.yml b/.github/workflows/harmony_scenic.yml
@@ -1,6 +1,6 @@
 name: harmony_scenic
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,26 +12,24 @@ on:
 
 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: |
-        mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz
-        tar xzvf sample_data_small.tar.gz
-        cp -r sample_data testdata/sample1
-        mv sample_data testdata/sample2
-    - name: Run harmony_scenic test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile harmony_scenic,test__harmony_scenic,test__compute_resources,docker -entry harmony_scenic -ansi-log false
-        cat .nextflow.log
-
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          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
+          wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_small.tar.gz
+          tar xzvf sample_data_small.tar.gz
+          cp -r sample_data testdata/sample1
+          mv sample_data testdata/sample2
+      - name: Run harmony_scenic test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile harmony_scenic,test__harmony_scenic,test__compute_resources,docker -entry harmony_scenic -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/mnncorrect.yml b/.github/workflows/mnncorrect.yml
@@ -1,6 +1,6 @@
 name: mnncorrect
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,24 +12,23 @@ on:
 
 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/
-    - name: Get sample data
-      run: |
-        mkdir testdata
-        wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data.tar.gz
-        tar xzvf sample_data.tar.gz
-        cp -r sample_data testdata/sample1
-        mv sample_data testdata/sample2
-    - name: Run single_sample test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile mnncorrect,test__mnncorrect,test__compute_resources,docker -entry mnncorrect -ansi-log false
-        cat .nextflow.log
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          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.tar.gz
+          tar xzvf sample_data.tar.gz
+          cp -r sample_data testdata/sample1
+          mv sample_data testdata/sample2
+      - name: Run single_sample test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile mnncorrect,test__mnncorrect,test__compute_resources,docker -entry mnncorrect -ansi-log false
+          cat .nextflow.log
diff --git a/.github/workflows/scenic.yml b/.github/workflows/scenic.yml
@@ -1,6 +1,6 @@
 name: scenic
 
-on: 
+on:
   push:
     branches:
       - master
@@ -12,18 +12,16 @@ on:
 
 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/
-    - name: Run scenic test
-      run: |
-        nextflow run ${GITHUB_WORKSPACE} -profile scenic,test__scenic,test__compute_resources,docker -entry scenic -ansi-log false
-        cat .nextflow.log
-
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER='21.04.3'
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Run scenic test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile scenic,test__scenic,test__compute_resources,docker -entry scenic -ansi-log false
+          cat .nextflow.log