GHA use shared singularity cache (#3738)

* Add Singularity cachedir for reducing storage footprint

* Use runner temp directory for reducing storage footprint

* Add default NXF directories for reducing memory footprint

* Replace variable with env because GHA scoping

* Add some fake stuff for triggering tests

* Remove working dir stuff.

* Create singularity dirs

* fixup

* Add more fake testing criteria

* Replace parabricks weird cp stuff with stageInMode directive

* parabricks/fq2bam: Replace copy in parabricks with stageInMode

The parabricks/fq2bam module had hard copies from the previous working dir to the local working directory to remove the affect of symlinks. However, this will fail on a number of cases therefore this commit replaces them with the stageInDirective of Nextflow.

* Revert deepvariant to nf-core image

* Revert "parabricks/fq2bam: Replace copy in parabricks with stageInMode"

This reverts commit f94d971.

* Revert "Replace parabricks weird cp stuff with stageInMode directive"

This reverts commit 44ed12a.

* Remove fake stuff from parabricks/fq2bam

* Ignore Singularity cache for uploading output(s)

* Fixup

.github/workflows/test.yml

@@ -13,6 +13,10 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
 jobs:
   prettier:
     runs-on: ubuntu-latest
@@ -251,6 +255,7 @@ jobs:
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+
     steps:
       - uses: actions/checkout@v3
 
@@ -289,6 +294,12 @@ jobs:
         with:
           singularity-version: 3.7.1
 
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
       - name: Set up miniconda
         if: matrix.profile == 'conda'
         uses: conda-incubator/setup-miniconda@v2
@@ -348,6 +359,7 @@ jobs:
             /home/runner/pytest_workflow_*/*/work
             !/home/runner/pytest_workflow_*/*/work/conda
             !/home/runner/pytest_workflow_*/*/work/singularity
+            !${{ github.workspace }}/.singularity
 
   nf-test-changes:
     name: nf-test-changes