diff --git a/i14/templates/xrf-tomo-template.yaml b/i14/templates/xrf-tomo-template.yaml index 9372d2e..ad697f0 100644 --- a/i14/templates/xrf-tomo-template.yaml +++ b/i14/templates/xrf-tomo-template.yaml @@ -39,7 +39,7 @@ spec: - name: normalise value: true - name: cor - value: "null" + value: "nil" - name: reconsMethod value: "FBP" volumeClaimTemplates: @@ -301,9 +301,9 @@ spec: mkdir -p $OUTPUT/httomo_output COR_ESTIMATE="{{`{{ inputs.parameters.initcor }}`}}" - [[ $COR_ESTIMATE != "null" ]] && sed -i 's//'"${COR_ESTIMATE}"'/' $OUTPUT/httomo.yaml + [[ $COR_ESTIMATE != "nil" ]] && sed -i 's//'"${COR_ESTIMATE}"'/' $OUTPUT/httomo.yaml COR="{{`{{ workflow.parameters.cor }}`}}" - [[ $COR != "null" ]] && sed -i 's/${{`{{centering.side_outputs.centre_of_rotation}}`}}/'"${COR}"'/' $OUTPUT/httomo.yaml + [[ $COR != "nil" ]] && sed -i 's/${{`{{centering.side_outputs.centre_of_rotation}}`}}/'"${COR}"'/' $OUTPUT/httomo.yaml cmd=(/opt/conda/bin/mpirun -n 1 /opt/conda/bin/python -m httomo run) cmd+=("--output-folder-name=${ELEMENT}-${TRANSITION}")