diff --git a/main.nf b/main.nf new file mode 100644 index 0000000..e69de29 diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000..e69de29 diff --git a/scripts/run_local.sh b/scripts/run_local.sh index 53cd161..4b8d4b5 100755 --- a/scripts/run_local.sh +++ b/scripts/run_local.sh @@ -2,11 +2,10 @@ set -e -# build component -rm -r target && viash ns build --parallel --setup cb +OUT=output/local # clear output dir -rm -r output/local +rm -r "$OUT" # run component NXF_VER=23.10.0 nextflow run \ @@ -15,7 +14,7 @@ NXF_VER=23.10.0 nextflow run \ -profile docker \ --input resources/input1.txt \ --multiple_input "resources/input1.txt;resources/input2.txt" \ - --publish_dir output/local + --publish_dir "$OUT" # check if output is correct -scripts/verify_output.sh output/local +scripts/verify_output.sh "$OUT" diff --git a/scripts/run_local_with_remote.sh b/scripts/run_local_with_remote.sh new file mode 100755 index 0000000..5c6f61f --- /dev/null +++ b/scripts/run_local_with_remote.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +set -e + +OUT=output/local_with_remote + +# clear output dir +rm -r "$OUT" + +# run component +NXF_VER=23.10.0 nextflow run \ + viash-io/test-nextflow-wave-fusion \ + -r main_build \ + -main-script target/nextflow/method/main.nf \ + -profile docker \ + --input resources/input1.txt \ + --multiple_input "resources/input1.txt;resources/input2.txt" \ + --publish_dir "$OUT" + +# check if output is correct +scripts/verify_output.sh "$OUT"