From afbb8311f7f3263f404c8df2d9ec62fdb63f0d26 Mon Sep 17 00:00:00 2001
From: Benedikt Daurer <benedikt.daurer@diamond.ac.uk>
Date: Mon, 24 Aug 2026 15:20:40 +0100
Subject: [PATCH 1/2] Avoid slash in mounted paths

---
 i14/templates/xrf-tomo-template.yaml | 30 ++++++++++++++--------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/i14/templates/xrf-tomo-template.yaml b/i14/templates/xrf-tomo-template.yaml
index 5dc4d73..30f3cde 100644
--- a/i14/templates/xrf-tomo-template.yaml
+++ b/i14/templates/xrf-tomo-template.yaml
@@ -66,7 +66,7 @@ spec:
       image: debian:stable-slim
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       command: [bash]
       source: |
         OUTPUT="{{`{{ workflow.parameters.visitdir }}`}}"/processing/workflows/"{{`{{ workflow.parameters.outputFolder }}`}}"
@@ -92,7 +92,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-stack-projections
@@ -104,7 +104,7 @@ spec:
       image: ghcr.io/diamondlightsource/nxstacker:latest
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
       env:
@@ -141,7 +141,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-copy-stacked-projections
@@ -153,7 +153,7 @@ spec:
       image: debian:stable-slim
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
       env:
@@ -186,7 +186,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-generate-shifts
@@ -223,14 +223,14 @@ spec:
 
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
     outputs:
       parameters:
       - name: initcor
         valueFrom:
-          path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/{{`{{ workflow.parameters.elementToAlign }}`}}-{{`{{ workflow.parameters.transitionToAlign }}`}}_cor.txt"
+          path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/{{`{{ workflow.parameters.elementToAlign }}`}}-{{`{{ workflow.parameters.transitionToAlign }}`}}_cor.txt"
       artifacts:
       - name: align_initial
         path: "/tmp/align_initial.html"
@@ -268,7 +268,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-align-and-normalise
@@ -308,7 +308,7 @@ spec:
 
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
     outputs:
@@ -345,7 +345,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-reconstruct
@@ -399,7 +399,7 @@ spec:
         
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
     outputs:
@@ -434,7 +434,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-plotting
@@ -467,7 +467,7 @@ spec:
 
       volumeMounts:
       - name: session
-        mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
       - name: tmp
         mountPath: /tmp
     outputs:
@@ -516,7 +516,7 @@ spec:
     volumes:
     - name: session
       hostPath:
-        path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}"
         type: Directory
 
   - name: xrf-tomo-alignment-pipeline

From c6c826f6c1826452545f6387bc23de51db4ffabb Mon Sep 17 00:00:00 2001
From: Benedikt Daurer <benedikt.daurer@diamond.ac.uk>
Date: Mon, 24 Aug 2026 15:36:23 +0100
Subject: [PATCH 2/2] Reverse artifact changes for httomo step

---
 i14/templates/xrf-tomo-template.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/i14/templates/xrf-tomo-template.yaml b/i14/templates/xrf-tomo-template.yaml
index 30f3cde..abfe763 100644
--- a/i14/templates/xrf-tomo-template.yaml
+++ b/i14/templates/xrf-tomo-template.yaml
@@ -376,11 +376,6 @@ spec:
         OUTPUT=$VISIT/processing/workflows/"{{`{{ workflow.parameters.outputFolder }}`}}"
         ELEMENT="{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}"
         TRANSITION="{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}"
-        mkdir -p $OUTPUT/httomo_output
-        mkdir -p $OUTPUT/httomo_output/${ELEMENT}-${TRANSITION}
-        mkdir -p /tmp/httomo_output
-
-        ln -s $OUTPUT/httomo_output/${ELEMENT}-${TRANSITION} /tmp/httomo_output/${ELEMENT}-${TRANSITION}
 
         COR_ESTIMATE="{{`{{ inputs.parameters.initcor }}`}}"
         [[ $COR_ESTIMATE != "nil" ]] && sed -i 's/<INITCOR>/'"${COR_ESTIMATE}"'/' $OUTPUT/httomo.yaml
@@ -405,7 +400,7 @@ spec:
     outputs:
       artifacts:
       - name: images32bit_tif
-        path: "/tmp/httomo_output/{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}-{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}/images32bit_tif"
+        path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/httomo_output/{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}-{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}/images32bit_tif"
 
     podSpecPatch: |
       containers: