feat(htsinfer): support Conda execution

.github/workflows/ci.yml

@@ -95,7 +95,7 @@ jobs:
         run: bash tests/test_integration_workflow/test.local.sh
 
       - name: Run htsinfer test script
-        run: bash tests/test_htsinfer_workflow/test.local.sh
+        run: bash tests/test_htsinfer_with_singularity/test.local.sh
 
       - name: Run SRA downloads workflow
         run: bash tests/test_sra_download_with_singularity/test.local.sh
@@ -208,6 +208,9 @@ jobs:
       - name: Run test script
         run: bash tests/test_integration_workflow_with_conda/test.local.sh
 
+      - name: Run htsinfer test script
+        run: bash tests/test_htsinfer_with_conda/test.local.sh
+
       - name: Run SRA downloads workflow
         run: bash tests/test_sra_download_with_conda/test.local.sh
 

tests/test_htsinfer_with_conda/test.local.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+# This script is currently exiting with non-zero status.
+# This is expected behaviour though, as several parameters can't be inferred from the test files.
+# Snakemake called with --keep-incomplete in order to keep the created samples table for inspection.
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    rm -rf .cache/
+    rm -rf .config/
+    rm -rf .fontconfig/
+    rm -rf .java/
+    rm -rf .snakemake/
+    rm -rf logs/
+    rm -rf results/
+    rm -rf Log.out
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
+set -u  # ensures that script exits when unset variables are used
+set -x  # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+    --snakefile="../../workflow/rules/htsinfer.smk" \
+    --restart-times=0 \
+    --profile="../../profiles/local-conda" \
+    --config outdir="results" \
+             samples="../input_files/htsinfer_samples.tsv" \
+             samples_out="samples_htsinfer.tsv" \
+             log_dir="logs" \
+             cluster_log_dir="logs/cluster_log" \
+    --notemp \
+    --keep-incomplete
+
+# Check md5 sum of some output files
+md5sum --check "expected_output.md5"

tests/test_htsinfer_with_singularity/expected_output.md5

@@ -0,0 +1,3 @@
+1dc3f566f896b72f8f0ab8b3d60da364  results/samples_htsinfer.tsv
+ca3f9ef26821bfa061d3b7708823ebc3  results/htsinfer_SRR1.json
+62303261f8dd73124c2a5a54cd28e572  results/htsinfer_SRR2.json

workflow/envs/htsinfer.yaml

@@ -2,5 +2,5 @@
 channels:
   - bioconda
 dependencies:
-  - htsinfer=0.10.0
+  - htsinfer=0.11.0
 ...

workflow/rules/htsinfer.smk

@@ -49,7 +49,7 @@ rule run_htsinfer:
         cluster_log_path=CLUSTER_LOG,
     threads: 4
     singularity:
-        "docker://zavolab/htsinfer:latest"
+        "docker://quay.io/biocontainers/htsinfer:0.11.0--pyhdfd78af_1"
     conda:
         os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml")
     log:
@@ -82,7 +82,7 @@ rule htsinfer_to_tsv:
         SAMPLES_OUT,
     threads: 4
     singularity:
-        "docker://zavolab/htsinfer:latest"
+        "docker://quay.io/biocontainers/htsinfer:0.11.0--pyhdfd78af_1"
     conda:
         os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml")
     log: