update custom targets for testing

.github/workflows/pipeline.yaml

@@ -25,7 +25,7 @@ on:
 jobs:
   #----------------------------------------------------------------------------#
   # Install dependencies
-  install :
+  pipeline :
     runs-on: ubuntu-latest
     steps:
       #------------------------------------------------------------------------#
@@ -59,14 +59,41 @@ jobs:
         run:
           mamba env create -f workflow/envs/default.yaml
       #------------------------------------------------------------------------#
-      #  Test pipeline
-      - name: test pipeline
+      # Test Database import rules
+      - name: test database import
         shell: bash -l {0}
         run:
           conda activate default;
-          snakemake all --use-conda --profile profiles/gh-actions;
-          snakemake --report report.html;
+          snakemake --use-conda --profile profiles/gh-actions test_sqlite_import_reference  test_sqlite_import_assembly test_sqlite_import_sra
           conda deactivate;
+      # Test Data Download
+      - name: test download
+        shell: bash -l {0}
+        run:
+          conda activate default;
+          snakemake --use-conda --profile profiles/gh-actions test_sqlite_import_reference test_download_sra test_download_fna test_download_ref
+          conda deactivate
+      # Test Alignment
+      - name: test download
+        shell: bash -l {0}
+        run:
+          conda activate default;
+          snakemake --use-conda --profile profiles/gh-actions test_sqlite_import_reference test_snippy_pairwise_fna test_eager_sra
+          conda deactivate
+      # Test Phylogeny
+      - name: test download
+        shell: bash -l {0}
+        run:
+          conda activate default;
+          snakemake --use-conda --profile profiles/gh-actions test_sqlite_import_reference test_iqtree
+          conda deactivate
+      # Test Report Generation
+      - name: test report
+        shell: bash -l {0}
+        run:
+          conda activate default;
+          snakemake --report report.html;
+          conda deactivate
       #------------------------------------------------------------------------#
       #  Artifact Upload
       - name: artifact report

workflow/Snakefile

@@ -38,6 +38,7 @@ include: "rules/download.smk"
 include: "rules/alignment.smk"
 include: "rules/phylogeny.smk"
 include: "rules/functions.smk"
+include: "rules/targets.smk"
 
 # Report file
 report: "report/workflow.rst"

workflow/rules/targets.smk

@@ -0,0 +1,52 @@
+
+# Custom targets for testing
+
+# Database Import
+rule test_sqlite_import_assembly:
+    input:
+        results_dir + "/sqlite_import/download_assembly.txt"
+
+rule test_sqlite_import_sra:
+    input:
+        results_dir + "/sqlite_import/eager_sra.tsv"
+
+rule test_sqlite_import_reference:
+    input:
+        results_dir + "/sqlite_import/download_assembly.txt"
+
+# Data Download
+rule test_download_sra:
+    input:
+        expand(results_dir + "/download_sra/{biosample}/{sra_acc}_1.fastq.gz",
+        zip,
+        biosample=identify_sra_sample()["biosample"],
+        sra_acc=identify_sra_sample()["sra_acc"])
+
+rule test_download_fna:
+    input:
+        expand(results_dir +"/download_assembly/{sample}.fna",
+        sample=identify_assembly_sample(),
+        )
+rule test_download_ref:
+    input:
+        expand(results_dir +"/download_reference/{sample}.fna",
+        sample=identify_reference_sample(),
+        )
+# Alignment
+rule test_eager_sra:
+    input:
+        expand(results_dir + "/eager_sra/damageprofiler/{sra_acc}_rmdup_{biosample}/DamagePlot.pdf",
+        zip,
+        sra_acc=identify_sra_sample()["sra_acc"],
+        biosample=identify_sra_sample()["biosample"])
+
+rule test_snippy_pairwise_fna:
+    input:
+        expand(results_dir + "/snippy_pairwise/{sample}/{sample}_snippy.aligned.fa",
+        sample=identify_assembly_sample())
+
+# Phylogeny
+rule test_iqtree:
+    input:
+        expand(results_dir + "/iqtree/iqtree.core-filter{missing_data}.treefile",
+        missing_data = config["snippy_missing_data"])