Merge pull request #94 from CCBR/ci-dryrun

Test a dryrun with GitHub Actions

.github/workflows/lintr.yaml

@@ -4,6 +4,11 @@ on:
     branches:
       - master
       - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
 jobs:
   Lintr:
     runs-on: ubuntu-latest
@@ -22,4 +27,4 @@ jobs:
         touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
         snakemake --lint -s /opt2/workflow/Snakefile \
         -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
-        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"
+        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"

.github/workflows/test_dev.yml

@@ -1,25 +1,32 @@
-name: DevTesting
+name: test
 on:
   push:
     branches:
+      - master
       - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4.1.0
     - uses: docker://snakemake/snakemake:v7.19.1
       with:
         directory: '.test'
-    - name: Dev Testing Workflow
-      continue-on-error: true
+    - name: dryrun
+      shell: bash {0}
       run: |
-        docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
-          "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \
-          cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \
-          cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \
-          cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \
-          cd /opt2/output_carlisle/annotation && \
-          touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
-          snakemake --lint -s /opt2/workflow/Snakefile \
-          -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
-          echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"
+        bash ./install.sh ./test-workdir/carlisle-v9999.9999.9999-dev
+        ./test-workdir/carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./test-workdir/output_carlisle
+        cp ./test-workdir/carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml ./test-workdir/output_carlisle/config/config.yaml
+        # TODO: use `carlisle run --mode dryrun`
+        docker run -v ./test-workdir/:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
+          "cd /opt2 && snakemake \
+            -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \
+            --dryrun \
+            --configfile carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml \
+            --directory output_carlisle"