Enable hard links in CI tests

vib-singlecell-nf · Jan 26, 2021 · 201c4ff · 201c4ff
1 parent 491ad8b
commit 201c4ff
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Showing 14 changed files with 14 additions and 0 deletions.
diff --git a/.github/workflows/bbknn.yml b/.github/workflows/bbknn.yml
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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_scenic.yml b/.github/workflows/single_sample_scenic.yml
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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
@@ -22,6 +22,7 @@ jobs:
         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