[RESOLVED] Executing multiple steps in recipe

Use Questions
1

If I have a recipe file and would like to execute a specific set of steps from the recipe, with one qunex_container call, is this the correct way to do that?

qunex_container run_recipe \
   --recipe_file="${STUDY_FOLDER}/processing/recipe.yaml" \
   --recipe="ncanda_hcp" \
   --bash_post="${BASH_POST}" \
   --bind="${STUDY_FOLDER}:${STUDY_FOLDER}" \
   --container="${QUNEX_CONTAINER}" \
   --steps="hcp_pre_freesurfer, hcp_freesurfer, hcp_post_freesurfer"

When I tried that, it only ran the first step. In the QuNex documentation, I see that specifying the steps parameter “is an alternative to specifying the recipe file and a recipe name.” Does this mean if I specify both a recipe file and steps, the qunex command will be confused? Sorry if this is a very basic question!

2

Hi delrubin,

Your line of thinking is correct. If you specify --steps along with the recipe file and the recipe name, then if will run a subset of commands/tasks. Can you try removing the spaces, the steps is a comma separated list, not a comma + space separated list, so:

--steps="hcp_pre_freesurfer,hcp_freesurfer,hcp_post_freesurfer"

This steps of course need to be present under the command list in the ncanda_hcp recipe.

Best, Jure

1 Like
3

Ah yes, the spaces were the issue. Thanks!