Avoid hard link in the publish process

.github/workflows/bbknn.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/bbknn_scenic.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/cell_annotate_filter.yml

@@ -22,7 +22,6 @@ 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 & dummy annotation
       run: |
         wget https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/sample_data_tiny.tar.gz

.github/workflows/decontx.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/harmony.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/mnncorrect.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/scenic.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/scenic_multiruns.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_decontx.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_decontx_scrublet.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_param_exploration.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_scenic.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_scenic_multiruns.yml

@@ -22,7 +22,6 @@ 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

.github/workflows/single_sample_scrublet.yml

@@ -22,7 +22,6 @@ 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

src/utils/processes/utils.nf

@@ -442,7 +442,7 @@ process SC__PUBLISH {
     input:
         tuple \
             val(tag), \
-            path(f), \
+            path(f, stageAs: 'input_file'), \
             val(stashedParams)
         val(fileOutputSuffix)
         val(toolName)
@@ -463,13 +463,9 @@ process SC__PUBLISH {
             isParameterExplorationModeOn,
             stashedParams
         )
-        /* avoid cases where the input and output files have identical names:
-           Move the input file to a unique name, then create a link to
-           the input file */
         """
-        mv $f tmp
         if [ ! -f ${outputFileName} ]; then
-            ln -L tmp "${outputFileName}"
+            ln -s input_file "${outputFileName}"
         fi
         """
 }