From 51f61670b8b8becf1bb481ded17e83614ba130f5 Mon Sep 17 00:00:00 2001
From: Karl5766 <karl29029@gmail.com>
Date: Fri, 4 Oct 2024 13:03:32 -0400
Subject: [PATCH] move args to rule

---
 spimquant/workflow/Snakefile            | 11 ++---------
 spimquant/workflow/rules/blobdetect.smk |  4 ++--
 2 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/spimquant/workflow/Snakefile b/spimquant/workflow/Snakefile
index b06b77b..16d9f9c 100644
--- a/spimquant/workflow/Snakefile
+++ b/spimquant/workflow/Snakefile
@@ -6,15 +6,8 @@ import shutil
 
 set_bids_spec("v0_11_0")
 
-TARGET_SNAKEBIDS_YML_PATH = pathlib.Path("config/snakebids.yml").resolve()  # configfile if found
-# otherwise use the template which will not directly work but you can provide command line arguments to add to it
-if not os.path.exists(TARGET_SNAKEBIDS_YML_PATH):
-    if not os.path.exists(TARGET_SNAKEBIDS_YML_PATH.parent):
-        os.makedirs(TARGET_SNAKEBIDS_YML_PATH.parent)
-    SNAKEBIDS_YML_PATH = "../examples/snakebids_template.yml"
-    shutil.copy(SNAKEBIDS_YML_PATH, TARGET_SNAKEBIDS_YML_PATH)
-
-configfile: TARGET_SNAKEBIDS_YML_PATH
+
+configfile: "config/snakebids.yml"
 
 
 # use expandvars so we can use e.g. '$SLURM_TMPDIR'
diff --git a/spimquant/workflow/rules/blobdetect.smk b/spimquant/workflow/rules/blobdetect.smk
index 4ba13e0..fd40273 100644
--- a/spimquant/workflow/rules/blobdetect.smk
+++ b/spimquant/workflow/rules/blobdetect.smk
@@ -311,8 +311,8 @@ rule negatively_masked_counting:
     Work in progress
     """
     input:
-        zarr=config["negatively_masked_counting"]["zarr"],
-        neg_mask=config["negatively_masked_counting"]["neg_mask"],
+        zarr='/path_to_bids_root/bids/sub-onuska21/micr/sub-onuska21_sample_brain_acq-prestitched_SPIM.ome.zarr?slices=[1]',
+        neg_mask='/path_to_bids_root/resources/onuska21_patched.tiff',
     params:
         neg_mask_scale=(1, 1, 1),
         tmp_path=f'{config["output_dir"]}/tmp'