set -e export NXF_PLUGINS_DEFAULT=nf-amazon # Skip test if AWS keys are missing if [[ ! $AWS_ACCESS_KEY_ID ]]; then echo "Skip s3-files test since AWS keys are not available" exit 0 fi # # run normal mode # $NXF_RUN | tee stdout [[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (gut)'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (liver)'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (lung)'` == 1 ]] || false cmp stdout .expected || false # # run resume mode # $NXF_RUN -resume | tee stdout [[ `grep INFO .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (gut)'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (liver)'` == 1 ]] || false [[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (lung)'` == 1 ]] || false cmp stdout .expected || false