linting

akhanf · Dec 23, 2022 · 48c5484 · 48c5484
1 parent 79abd53
commit 48c5484
Show file tree

Hide file tree

Showing 4 changed files with 49 additions and 11 deletions.
diff --git a/snakedwi/workflow/Snakefile b/snakedwi/workflow/Snakefile
@@ -21,13 +21,24 @@ rule all:
         **get_eddy_quad_all(),
         **get_bedpost_all(),
         mask_qc=expand(
-            bids(root=root,datatype='qc', suffix="mask.png", desc="brain", **subj_wildcards),
+            bids(
+                root=root,
+                datatype="qc",
+                suffix="mask.png",
+                desc="brain",
+                **subj_wildcards
+            ),
             zip,
             **input_zip_lists["dwi"]
         ),
         reg_qc=expand(
             bids(
-                root=root,datatype='qc', suffix="reg.png", from_="dwiref", to="T1w", **subj_wildcards
+                root=root,
+                datatype="qc",
+                suffix="reg.png",
+                from_="dwiref",
+                to="T1w",
+                **subj_wildcards
             ),
             zip,
             **input_zip_lists["dwi"]

diff --git a/snakedwi/workflow/rules/prepdwi.smk b/snakedwi/workflow/rules/prepdwi.smk
@@ -719,11 +719,23 @@ rule qc_brainmask_for_eddy:
         seg=get_mask_for_eddy(),
     output:
         png=report(
-            bids(root=root,datatype='qc', suffix="mask.png", desc="brain", **subj_wildcards),
+            bids(
+                root=root,
+                datatype="qc",
+                suffix="mask.png",
+                desc="brain",
+                **subj_wildcards
+            ),
             caption="../report/brainmask_dwi.rst",
             category="Brainmask",
         ),
-        html=bids(root=root,datatype='qc', suffix="mask.html", desc="brain", **subj_wildcards),
+        html=bids(
+            root=root,
+            datatype="qc",
+            suffix="mask.html",
+            desc="brain",
+            **subj_wildcards
+        ),
     group:
         "subj"
     container:

diff --git a/snakedwi/workflow/rules/reg_dwi_to_t1.smk b/snakedwi/workflow/rules/reg_dwi_to_t1.smk
@@ -103,13 +103,23 @@ rule qc_reg_dwi_t1:
     output:
         png=report(
             bids(
-                root=root,datatype='qc', suffix="reg.png", **subj_wildcards, from_="dwiref", to="T1w"
+                root=root,
+                datatype="qc",
+                suffix="reg.png",
+                **subj_wildcards,
+                from_="dwiref",
+                to="T1w"
             ),
             caption="../report/reg_dwi_t1.rst",
             category="B0 T1w registration",
         ),
         html=bids(
-            root=root,datatype='qc', suffix="reg.html", from_="dwiref", to="T1w", **subj_wildcards
+            root=root,
+            datatype="qc",
+            suffix="reg.html",
+            from_="dwiref",
+            to="T1w",
+            **subj_wildcards
         ),
     group:
         "subj"

diff --git a/snakedwi/workflow/rules/visqc.smk b/snakedwi/workflow/rules/visqc.smk
@@ -12,7 +12,8 @@ rule qc_reg:
     output:
         png=report(
             bids(
-                root=root,datatype='qc',
+                root=root,
+                datatype="qc",
                 subject="{subject}",
                 suffix="regqc.png",
                 from_="subject",
@@ -24,7 +25,8 @@ rule qc_reg:
             subcategory="{desc} {template}",
         ),
         html=bids(
-            root=root,datatype='qc',
+            root=root,
+            datatype="qc",
             subject="{subject}",
             suffix="regqc.html",
             from_="subject",
@@ -51,7 +53,8 @@ rule qc_probseg:
     output:
         png=report(
             bids(
-                root=root,datatype='qc',
+                root=root,
+                datatype="qc",
                 subject="{subject}",
                 suffix="probseg.png",
                 desc="atropos3seg",
@@ -82,7 +85,8 @@ rule qc_dseg:
     output:
         png=report(
             bids(
-                root=root,datatype='qc',
+                root=root,
+                datatype="qc",
                 subject="{subject}",
                 suffix="dseg.png",
                 atlas="{atlas}",
@@ -93,7 +97,8 @@ rule qc_dseg:
             subcategory="{atlas} Atlas from {template}",
         ),
         html=bids(
-            root=root,datatype='qc',
+            root=root,
+            datatype="qc",
             subject="{subject}",
             suffix="dseg.html",
             atlas="{atlas}",