From e7ce120e1e1e792d4cdee62392edc230c933dd62 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 2 Jun 2026 13:11:10 +0200 Subject: [PATCH 1/3] Include local resources by default --- nextflow.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nextflow.config b/nextflow.config index 7a6ff17..f604f02 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,6 +16,9 @@ params { monochrome_logs = false } +// Include local resources by default +includeConfig "$baseDir/config/resources/local.config" + profiles { itrop { From 4f325419eee0b6b33a255c7158a440e7bdbed264 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 2 Jun 2026 13:15:47 +0200 Subject: [PATCH 2/3] Include local resources by default --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index f604f02..f737da8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,7 +17,7 @@ params { } // Include local resources by default -includeConfig "$baseDir/config/resources/local.config" +includeConfig "$baseDir/config/ressources/local.config" profiles { From 5c1fe06bead811f73f20b0f72dd02471ea84c9ef Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 2 Jun 2026 13:42:33 +0200 Subject: [PATCH 3/3] Implement Docker cleanup after test executions Added cleanup steps to free disk space after each test run. --- .github/workflows/main.yml | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9ea9ff0..5c5bfd8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -56,18 +56,50 @@ jobs: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - uses: actions/checkout@v3 + + - name: Free disk space + run: | + docker system prune -af || true + sudo rm -rf /usr/share/dotnet /opt/ghc /usr/local/lib/android || true + sudo apt-get clean + df -h + # Run tests sequentialy - name: test short single run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test short single cram run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --cram --filter_unmapped + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test short paired run: nextflow run -ansi-log -profile docker,test_illumina_paired aline.nf + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test ont run: nextflow run -ansi-log -profile docker,test_ont aline.nf + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test pacbio run: nextflow run -ansi-log -profile docker,test_pacbio aline.nf + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test csv run: nextflow run -ansi-log -profile docker,test_csv aline.nf + + - name: Cleanup Docker + run: docker system prune -af || true + - name: test remote run: nextflow run -ansi-log -profile docker,test_remote aline.nf