From cb08829c668f5b0496b720a43149055f81e80a0d Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Tue, 13 Feb 2024 12:05:10 -0500
Subject: [PATCH] add logs for linting

---
 workflow/rules/atlasreg.smk | 49 +++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/workflow/rules/atlasreg.smk b/workflow/rules/atlasreg.smk
index 1c7da67..5124e8a 100644
--- a/workflow/rules/atlasreg.smk
+++ b/workflow/rules/atlasreg.smk
@@ -8,6 +8,8 @@ rule import_anat:
         anat=lambda wildcards: config["atlases"][wildcards.template]["anat"],
     output:
         anat=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+    log:
+        bids_tpl(root='logs',datatype="import_anat",template="{template}", suffix="log.txt")
     shell:
         "cp {input} {output}"
 
@@ -17,6 +19,8 @@ rule import_dseg:
         dseg=lambda wildcards: config["atlases"][wildcards.template]["dseg"],
     output:
         dseg=bids_tpl(root=root, template="{template}", suffix="dseg.nii.gz"),
+    log:
+        bids_tpl(root='logs',datatype="import_dseg",template="{template}", suffix="log.txt")
     shell:
         "cp {input} {output}"
 
@@ -26,6 +30,8 @@ rule import_lut:
         json=lambda wildcards: config["atlases"][wildcards.template]["lut"],
     output:
         tsv=bids_tpl(root=root, template="{template}", suffix="dseg.tsv"),
+    log:
+        bids_tpl(root='logs',datatype="import_lut",template="{template}", suffix="log.txt")
     script:
         "../scripts/import_labelmapper_lut.py"
 
@@ -67,6 +73,16 @@ rule affine_reg:
             desc="affinewarped",
             suffix="spim.nii",
         ),
+    log:
+        bids(
+            root='logs',
+            subject="{subject}",
+            datatype="affine_reg",
+            sample="{sample}",
+            acq="{acq}",
+            space="{template}",
+            suffix="log.txt",
+        ),
     shell:
         "greedy -d 3 -i {input.template} {input.subject} "
         " -a -dof 12 -ia-image-centers -m NMI -o {output.xfm_ras} && "
@@ -111,6 +127,16 @@ rule deform_reg:
             desc="deformwarped",
             suffix="spim.nii",
         ),
+    log:
+        bids(
+            root='logs',
+            subject="{subject}",
+            datatype="deform_reg",
+            sample="{sample}",
+            acq="{acq}",
+            space="{template}",
+            suffix="log.txt",
+        ),
     shell:
         "greedy -d 3 -i {input.template} {input.subject} "
         " -it {input.xfm_ras} -m NMI "
@@ -150,6 +176,18 @@ rule resample_labels_to_zarr:
                 )
             )
         ),
+    log:
+        bids(
+            root='logs',
+            subject="{subject}",
+            datatype="resample_labels_to_zarr",
+            sample="{sample}",
+            acq="{acq}",
+            desc="{desc}",
+            space="{template}",
+            suffix="log.txt",
+        ),
+
     script:
         "../scripts/resample_labels_to_zarr.py"
 
@@ -194,5 +232,16 @@ rule zarr_to_ome_zarr_labels:
         config["containers"]["spimprep"]
     group:
         "preproc"
+    log:
+        bids(
+            root='logs',
+            subject="{subject}",
+            datatype="zarr_to_ome_zarr_labels",
+            sample="{sample}",
+            acq="{acq}",
+            desc="{desc}",
+            space="{template}",
+            suffix="log.txt",
+        ),
     script:
         "../scripts/zarr_to_ome_zarr_labels.py"