From c63d251ac8cca1c5ae8b4ded4d087711de7e02f0 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Thu, 8 Feb 2024 15:17:54 -0800 Subject: [PATCH] gzip reads and add pipeline run to workflow --- .github/scripts/simulate_reads.sh | 6 ++++++ .github/workflows/pull_request.yml | 2 ++ 2 files changed, 8 insertions(+) diff --git a/.github/scripts/simulate_reads.sh b/.github/scripts/simulate_reads.sh index 8169f81..592c8ee 100755 --- a/.github/scripts/simulate_reads.sh +++ b/.github/scripts/simulate_reads.sh @@ -20,3 +20,9 @@ art_illumina \ --qShift 0 \ --qShift2 0 \ --out .github/data/fastq/NC000962.3_R + +mv .github/data/fastq/NC000962.3_R1.fq .github/data/fastq/NC000962.3_R1.fastq +mv .github/data/fastq/NC000962.3_R2.fq .github/data/fastq/NC000962.3_R2.fastq + +gzip .github/data/fastq/NC000962.3_R1.fastq +gzip .github/data/fastq/NC000962.3_R2.fastq diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 6076784..ad8d565 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -27,6 +27,8 @@ jobs: run: bash .github/scripts/download_assemblies.sh - name: Simulate Reads run: bash .github/scripts/simulate_reads.sh + - name: Run Pipeline + run: bash .github/scripts/run_pipeline.sh - name: Upload Artifacts uses: actions/upload-artifact@v4 if: always()