diff --git a/validation/run-all.sh b/validation/run-all.sh index dbf41dc..81867e0 100755 --- a/validation/run-all.sh +++ b/validation/run-all.sh @@ -6,12 +6,16 @@ BUILD=0 SKIPLOCAL=0 NFAZURE=0 NFSUN=0 +NFSLEEP=0 +NFDEMO=0 [[ "$@" =~ '--build' ]] && BUILD=1 [[ -f $HOME/.nextflow/plugins/nf-nomad-latest/ ]] && BUILD=1 [[ "$@" =~ '--skiplocal' ]] && SKIPLOCAL=1 [[ "$@" =~ '--nfazure' ]] && NFAZURE=1 [[ "$@" =~ '--nfsun' ]] && NFSUN=1 +[[ "$@" =~ '--sleep' ]] && NFSLEEP=1 +[[ "$@" =~ '--demo' ]] && NFDEMO=1 if [ "$BUILD" == 1 ]; then pushd .. @@ -66,15 +70,23 @@ fi #NOTE2: You need to have 2 secrets stored in your Nextlow: SUN_NOMADLAB_ACCESS_KEY and SUN_NOMADLAB_SECRET_KEY if [ "$NFSUN" == 1 ]; then - nextflow run -w s3://juicefs/integration-test -c sun-nomadlab/nextflow.config hello + if [ "$NFSLEEP" == 1 ]; then + nextflow run -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config abhi18av/nf-sleep --timeout 360 - nextflow run bactopia/bactopia \ - -w s3://juicefs/integration-test -c sun-nomadlab/nextflow.config \ - -profile test,docker --outdir s3://juicefs/bactopia/outdir \ - --accession SRX4563634 --coverage 100 --genome_size 2800000 \ - --datasets_cache s3://juicefs/bactopia/assets + elif [ "$NFDEMO" == 1 ]; then + nextflow run nf-core/demo \ + -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config \ + -profile test,docker --outdir s3://fusionfs/integration-test/nf-core-demo/outdir + else + nextflow run -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config hello + nextflow run bactopia/bactopia \ + -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config \ + -profile test,docker --outdir s3://fusionfs/integration-test/bactopia/outdir \ + --accession SRX4563634 --coverage 100 --genome_size 2800000 \ + --datasets_cache s3://fusionfs/integration-test/bactopia/assets + fi else echo "skip nfsun" -fi \ No newline at end of file +fi diff --git a/validation/sun-nomadlab/nextflow.config b/validation/sun-nomadlab/nextflow.config index 5ff7c27..5affd7b 100644 --- a/validation/sun-nomadlab/nextflow.config +++ b/validation/sun-nomadlab/nextflow.config @@ -30,7 +30,7 @@ nomad { } jobs { - deleteOnCompletion = true + deleteOnCompletion = false volumes = [ { type "csi" name "juicefs-volume" } ]