set -e # # run normal mode # echo '' $NXF_RUN --alpha uno --beta \* --delta 'x_{1,2}.fasta' --gamma hello\ world --omega '--foo bar' a b c | tee stdout < stdout grep -F 'alpha: uno' < stdout grep -F 'beta : *' < stdout grep -F 'delta: x_{1,2}.fasta' < stdout grep -F 'gamma: hello world' < stdout grep -F 'omega: --foo bar' < stdout grep -F 'args : a_b_c' # # check quotes # echo '' $NXF_RUN --alpha "a'b" --beta 'a"b' --delta 'x' --gamma "x" --omega x "a b c" | tee stdout < stdout grep -F "alpha: a'b" < stdout grep -F 'beta : a"b' < stdout grep -F 'delta: x' < stdout grep -F 'gamma: x' < stdout grep -F 'omega: x' < stdout grep -F 'args : a b c' # # check the log command handle properly quoted filter options # $NXF_CMD -log .nextflow.log log last -F 'container = "ubuntu"' | tee log [[ $? == 0 ]] || exit 1 $NXF_CMD -log .nextflow.log log last -F "container = 'ubuntu'" | tee log [[ $? == 0 ]] || exit 1