diff --git a/.gitignore b/.gitignore index 89f1c863..442322d4 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,4 @@ params.yaml *.old null quilt+* +nextflow diff --git a/Makefile b/Makefile index 2257631c..888bf6a5 100644 --- a/Makefile +++ b/Makefile @@ -3,6 +3,7 @@ PROJECT ?= nf-quilt WRITE_BUCKET ?= quilt-example FRAGMENT ?= &path=. NF_DIR ?= ../nextflow +NF_BIN ?= ./nextflow PID ?= $$$$ PIPELINE ?= sarek QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com @@ -35,7 +36,11 @@ compile: ./gradlew compileGroovy exportClasspath @echo "DONE `date`" -nextflow: +$(NF_BIN): + curl -s https://get.nextflow.io | bash + chmod +x $(NF_BIN) + +nextflow-git: if [ ! -d "$(NF_DIR)" ]; then git clone https://github.com/nextflow-io/nextflow.git "$(NF_DIR)"; fi cd "$(NF_DIR)"; git checkout && make compile && git restore .; cd .. @@ -48,7 +53,7 @@ check: test: clean compile check #coverage -test-nextflow: clean nextflow compile check #coverage +test-nextflow: clean nextflow-git compile check #coverage test-all: clean compile-all check #coverage @@ -64,15 +69,15 @@ pkg-fail: compile echo "$(TEST_URI)" ./launch.sh run ./fail.nf -profile standard -plugins $(PROJECT) --outdir "$(TEST_URI)" -tower-test: compile-all - nextflow run "https://github.com/quiltdata/nf-quilt" -name local_einstein -with-tower -r main -latest --pub "$(TEST_URI)" +tower-test: $(NF_BIN) + $(NF_BIN) run "https://github.com/quiltdata/nf-quilt" -name local_einstein -with-tower -r main -latest --pub "$(TEST_URI)" # use `make $(PIPELINE) WRITE_BUCKET=my-s3-bucket` to publish `--outdir` to a Quilt package -$(PIPELINE): compile install +$(PIPELINE): $(NF_BIN) install echo "Ensure you have docker running" - nextflow pull nf-core/$(PIPELINE) - nextflow run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(QUILT_URI)" + $(NF_BIN) pull nf-core/$(PIPELINE) + $(NF_BIN) run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(QUILT_URI)" # # Show dependencies