Add pipeline running script

BCCDC-PHL · Feb 8, 2024 · 54ce545 · 54ce545
1 parent d0e3dbe
commit 54ce545
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diff --git a/.github/scripts/create_art_environment.sh b/.github/scripts/create_art_environment.sh
diff --git a/.github/scripts/download_assemblies.sh b/.github/scripts/download_assemblies.sh
diff --git a/.github/scripts/install_conda.sh b/.github/scripts/install_conda.sh
diff --git a/.github/scripts/install_nextflow.sh b/.github/scripts/install_nextflow.sh
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+nextflow run main.nf \
+	 -profile conda \
+	 --cache ${HOME}/.conda/envs \
+	 --fastq_input .github/data/fastq \
+	 --outdir .github/data/test_output \
+	 -with-report .github/data/test_output/nextflow_report.html \
+ 	 -with-trace .github/data/test_output/nextflow_trace.tsv
diff --git a/.github/scripts/simulate_reads.sh b/.github/scripts/simulate_reads.sh
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -18,6 +18,8 @@ jobs:
     - name: Install Miniconda
       run: bash .github/scripts/install_conda.sh
     - name: Install Nextflow
+      env:
+        NXF_VER: ${{ matrix.nextflow_version }}
       run: bash .github/scripts/install_nextflow.sh
     - name: Create ART Read-Simulation Environment
       run: bash .github/scripts/create_art_environment.sh