From 1ca8bbb075cc241e6b68a9ba7e61c5db590a0cbe Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 3 Nov 2023 14:08:47 -0400
Subject: [PATCH] RF: Move confounds datasink into bold_wf

---
 fmriprep/workflows/bold/base.py    | 17 +++++++++++++++++
 fmriprep/workflows/bold/outputs.py | 14 --------------
 2 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index a750e951d..99e75aecc 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -452,6 +452,19 @@ def init_bold_wf(
         name="bold_confounds_wf",
     )
 
+    ds_confounds = pe.Node(
+        DerivativesDataSink(
+            base_directory=fmriprep_dir,
+            desc='confounds',
+            suffix='timeseries',
+            dismiss_entities=("echo",),
+        ),
+        name="ds_confounds",
+        run_without_submitting=True,
+        mem_gb=DEFAULT_MEMORY_MIN_GB,
+    )
+    ds_confounds.inputs.source_file = bold_file
+
     workflow.connect([
         (inputnode, bold_confounds_wf, [
             ('t1w_tpms', 'inputnode.t1w_tpms'),
@@ -467,6 +480,10 @@ def init_bold_wf(
         (bold_native_wf, bold_confounds_wf, [
             ('outputnode.bold_native', 'inputnode.bold'),
         ]),
+        (bold_confounds_wf, ds_confounds, [
+            ('outputnode.confounds_file', 'in_file'),
+            ('outputnode.confounds_metadata', 'meta_dict'),
+        ]),
     ])  # fmt:skip
 
     # Fill-in datasinks of reportlets seen so far
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index 9f141f17c..d31cafc0b 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/fmriprep/workflows/bold/outputs.py
@@ -961,17 +961,6 @@ def init_func_derivatives_wf(
     raw_sources = pe.Node(niu.Function(function=_bids_relative), name='raw_sources')
     raw_sources.inputs.bids_root = bids_root
 
-    ds_confounds = pe.Node(
-        DerivativesDataSink(
-            base_directory=output_dir,
-            desc='confounds',
-            suffix='timeseries',
-            dismiss_entities=("echo",),
-        ),
-        name="ds_confounds",
-        run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
     ds_ref_t1w_xfm = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
@@ -1001,9 +990,6 @@ def init_func_derivatives_wf(
     # fmt:off
     workflow.connect([
         (inputnode, raw_sources, [('all_source_files', 'in_files')]),
-        (inputnode, ds_confounds, [('source_file', 'source_file'),
-                                   ('confounds', 'in_file'),
-                                   ('confounds_metadata', 'meta_dict')]),
         (inputnode, ds_ref_t1w_xfm, [('source_file', 'source_file'),
                                      ('bold2anat_xfm', 'in_file')]),
         (inputnode, ds_ref_t1w_inv_xfm, [('source_file', 'source_file'),