Partially revert "DOC/RF: Improve graph intelligibility"

This partially reverts commit 617b2a1.

Author: effigies

fmriprep/workflows/bold/fit.py

@@ -342,6 +342,7 @@ def init_bold_fit_wf(
         config.loggers.workflow.info("Stage 1: Adding HMC boldref workflow")
         hmc_boldref_wf = init_raw_boldref_wf(
             name="hmc_boldref_wf",
+            bold_file=bold_file,
             multiecho=multiecho,
         )
         hmc_boldref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
@@ -356,7 +357,6 @@ def init_bold_fit_wf(
 
         # fmt:off
         workflow.connect([
-            (inputnode, hmc_boldref_wf, [('bold_file', 'inputnode.bold_file')]),
             (hmc_boldref_wf, hmcref_buffer, [
                 ("outputnode.bold_file", "bold_file"),
                 ("outputnode.boldref", "boldref"),

fmriprep/workflows/bold/reference.py

@@ -30,6 +30,7 @@
 
 
 def init_raw_boldref_wf(
+    bold_file=None,
     multiecho=False,
     name="raw_boldref_wf",
 ):
@@ -52,6 +53,8 @@ def init_raw_boldref_wf(
 
     Parameters
     ----------
+    bold_file : :obj:`str`
+        BOLD series NIfTI file
     multiecho : :obj:`bool`
         If multiecho data was supplied, data from the first echo will be selected
     name : :obj:`str`
@@ -103,6 +106,10 @@ def init_raw_boldref_wf(
         name="outputnode",
     )
 
+    # Simplify manually setting input image
+    if bold_file is not None:
+        inputnode.inputs.bold_file = bold_file
+
     val_bold = pe.Node(
         ValidateImage(),
         name="val_bold",