feat!: set nifti_4D to FALSE (madym default), except for ETM

UoMResearchIT · Sep 17, 2024 · 370539a · 370539a
1 parent 7138bae
commit 370539a
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Showing 4 changed files with 6 additions and 25 deletions.
diff --git a/tools/madym_DCE.cwl b/tools/madym_DCE.cwl
@@ -17,8 +17,6 @@ doc: |
 
     NOTES:
       - The following override the madym_DCE defaults:
-        - `nifti_4D` defaults to TRUE for NIFTI and NIFTI_GZ `img_fmt_r`
-        - `nifti_scaling` defaults to TRUE
         - `use_BIDS` defaults to TRUE
         - `img_fmt_r` defaults to `NIFTI_GZ`
         - `img_fmt_w`is set to track `img_fmt_r`
@@ -81,18 +79,11 @@ inputs:
   nifti_4D:
     label: Read NIFTI 4D images for T1 mapping and dynamic inputs? 
     doc: |
-      Default is TRUE for NIFTI and NIFTI_GZ `img_fmt_r`.
       If set, the following arguments are ignored (see `dyn`):
       `n_dyns`, `sequence_format`, `sequence_start`, `sequence_step`
-    type: 
-      - boolean
-      - type: enum
-        symbols: [ "auto" ]
-    default: "auto"
+    type: boolean?
     inputBinding:
       prefix: --nifti_4D
-      valueFrom: |
-        $(self !== "auto" ? self: inputs.img_fmt_r.startsWith("NIFTI"))
   dyn_dir:
     label: Folder containing dynamic volumes
     type: Directory

diff --git a/tools/madym_T1.cwl b/tools/madym_T1.cwl
@@ -17,8 +17,6 @@ doc: |
 
     NOTES:
       - The following override the madym_T1 defaults:
-        - `nifti_4D` defaults to TRUE for NIFTI and NIFTI_GZ `img_fmt_r`
-        - `nifti_scaling` defaults to TRUE
         - `use_BIDS` defaults to TRUE
         - `img_fmt_r` defaults to `NIFTI_GZ`
         - `img_fmt_w`is set to track `img_fmt_r`
@@ -155,17 +153,9 @@ inputs:
       prefix: --err
   nifti_4D:
     label: Read NIFTI 4D images for T1 mapping and dynamic inputs? 
-    doc: |
-      Default is TRUE for NIFTI and NIFTI_GZ `img_fmt_r`.
-    type: 
-      - boolean
-      - type: enum
-        symbols: [ "auto" ]
-    default: "auto"
+    type: boolean?
     inputBinding:
       prefix: --nifti_4D
-      valueFrom: |
-        $(self !== "auto" ? self: inputs.img_fmt_r.startsWith("NIFTI"))
   nifti_scaling:
     label: Apply intensity scaling and offset when reading/writing NIFTI images
     type: boolean?

diff --git a/workflows/DCE_VFA.cwl b/workflows/DCE_VFA.cwl
@@ -9,7 +9,7 @@ doc: |
     3. Fits a tracer-kinetic model to DCE time-series data (using VFA T1 map).
 
     NOTES:
-        - `nifti_4D` is hard-set to TRUE (required for OE_deltaR1.cwl)
+        - `nifti_4D` is hard-set to TRUE for ETM, FALSE for VFA
         - `img_fmt_r`/`img_fmt_w` are hard-set to `NIFTI_GZ` (id.)
 requirements:
   InlineJavascriptRequirement: {}
@@ -186,7 +186,7 @@ steps:
       TR: TR
       roi: roi
       nifti_4D:
-        default: true
+        default: false
       img_fmt_r:
         default: NIFTI_GZ
       nifti_scaling: nifti_scaling

diff --git a/workflows/OE_IR.cwl b/workflows/OE_IR.cwl
@@ -7,7 +7,7 @@ doc: |
     then compares the average R1(t) for the baseline and enhancing periods.
 
     NOTES:
-        - `nifti_4D` is hard-set to TRUE (required for OE_deltaR1.cwl)
+        - `nifti_4D` is hard-set to FALSE
         - `img_fmt_r`/`img_fmt_w` are hard-set to `NIFTI_GZ` (id.)
 
 requirements:
@@ -116,7 +116,7 @@ steps:
       T1_init_params: T1_init_params
       roi: roi
       nifti_4D:
-        default: true
+        default: false
       img_fmt_r:
         default: NIFTI_GZ
       nifti_scaling: nifti_scaling