Force creation of .snakebids file (#192)

Fixes error when running on existing and adds a test case
khanlab · Jun 3, 2022 · 84f6cd3 · 84f6cd3
1 parent 201d2a5
commit 84f6cd3
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diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
@@ -122,6 +122,10 @@ jobs:
     - name: Test single T2w bids
       run: |
         poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
+    - name: Test running on existing folder
+      run: |
+        mkdir test_newout
+        poetry run hippunfold test_data/bids_singleT2w test_newout participant -np --modality T2w
     - name: Test single T2w bids, right hemi
       run: |
         poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R

diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -1,6 +1,8 @@
 bids_dir: '../test_data/bids_singleT2w'
 output_dir: 'test_output' #don't use '.'
 
+force: True
+
 #snakemake_dir: '.' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI
 
 #enable printing debug statements during parsing -- disable if generating dag visualization