REGISTRATION overhaul !

.devcontainer/devops/Dockerfile

@@ -67,3 +67,5 @@ RUN pipx ensurepath && \
 # Export history for saving between container sessions
 RUN SNIPPET="export PROMPT_COMMAND='history -a' && export HISTFILE=/home/$USERNAME/commandhistory/.bash_history" \
     && echo "$SNIPPET" >> "/home/$USERNAME/.bashrc"
+
+ENTRYPOINT ["/bin/sh", "-lc", "pipx ensurepath && exec \"$@\""]

.github/workflows/lint_component.yml

@@ -45,33 +45,24 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Setup Python
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
         with:
-          attempt_delay: 5000
-          action: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
-          with: |
-            python-version: "3.10"
+          python-version: "3.10"
 
       - uses: abatilo/actions-poetry@7b6d33e44b4f08d7021a1dee3c044e9c253d6439 # v3.0.0
         with:
           poetry-version: "1.8.*"
 
       - name: Setup Java
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4.7.1
         with:
-          attempt_delay: 5000
-          action: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4.7.1
-          with: |
-            distribution: "temurin"
-            java-version: "17"
+          distribution: "temurin"
+          java-version: "17"
 
       - name: Setup nextflow
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0
         with:
-          attempt_delay: 5000
-          action: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0
-          with: |
-            version: ${{ inputs.nextflow_version }}
+          version: ${{ inputs.nextflow_version }}
 
       - name: Install nf-core tools
         run: |

.github/workflows/run_checks_suite.yml

@@ -6,7 +6,7 @@ on:
         description: "Nextflow version to use"
         required: false
         type: string
-        default: "24.04.4"
+        default: "25.04.6"
       nf_core_version:
         description: "nf-core version to use"
         required: false
@@ -25,13 +25,10 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Setup Python
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
         with:
-          attempt_delay: 5000
-          action: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
-          with: |
-            python-version: "3.11"
-            cache: "pip"
+          python-version: "3.11"
+          cache: "pip"
 
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         # FIXME Flip this off once we get to less than a couple hundred. Adding
@@ -46,13 +43,10 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Setup Node
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
         with:
-          attempt_delay: 5000
-          action: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
-          with: |
-            node-version: "20"
-            cache: "npm"
+          node-version: "20"
+          cache: "npm"
 
       - name: Install Prettier
         run: npm ci
@@ -66,13 +60,10 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Setup Node
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
         with:
-          attempt_delay: 5000
-          action: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
-          with: |
-            node-version: "20"
-            cache: "npm"
+          node-version: "20"
+          cache: "npm"
 
       - name: Install editorconfig-checker
         run: npm ci
@@ -193,13 +184,7 @@ jobs:
           - runner: scilus-docker-large
             path: modules/nf-neuro/betcrop/synthbet
           - runner: scilus-docker-large
-            path: modules/nf-neuro/registration/synthregistration
-          - runner: scilus-docker-large
-            path: subworkflows/nf-neuro/preproc_t1
-          - runner: scilus-docker-large
-            path: subworkflows/nf-neuro/registration
-          - runner: scilus-docker-large
-            path: subworkflows/nf-neuro/anatomical_segmentation
+            path: modules/nf-neuro/registration/synthmorph
         exclude:
           - path: subworkflows/nf-neuro/load_test_data
     uses: ./.github/workflows/test_component.yml

.github/workflows/test_component.yml

@@ -77,30 +77,22 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Setup Python
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
         with:
-          attempt_delay: 5000
-          action: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
-          with: |
-            python-version: "3.11"
-            cache: "pip"
+          python-version: "3.11"
+          cache: "pip"
 
       - name: Setup Java
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4.7.1
         with:
-          attempt_delay: 5000
-          action: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4.7.1
-          with: |
-            distribution: "temurin"
-            java-version: "17"
+          distribution: "temurin"
+          java-version: "17"
 
       - name: Setup nextflow
-        uses: Wandalen/wretry.action@v3.7.2
+        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0
         with:
-          attempt_delay: 5000
-          action: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0
-          with: |
-            version: ${{ inputs.nextflow_version }}
+          version: ${{ inputs.nextflow_version }}
+
       - uses: nf-core/setup-nf-test@fbd9d701dd1f41a38b151a737a0f12e97f3c4c56 # v1.3.5
         with:
           version: ${{ inputs.nf_test_version }}
@@ -197,27 +189,6 @@ jobs:
           retention-days: 1
           compression-level: 9
 
-      - name: Collect test working directories
-        if: failure()
-        run: |
-          mkdir -p tests_workdir
-          for t in ${{ env.NXF_WORKDIR }}/.nf-test/tests/**/work/**/.command.log
-          do
-            tag=$(sed -n '3p' $(dirname $t)/.command.run | cut -d' ' -f3 | tr -d "'")
-            cp -R $(dirname $t) tests_workdir/$tag
-          done
-
-      - name: Upload test working directories
-        if: failure()
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
-        with:
-          name: tests-workdir-${{ steps.test-run-identifier.outputs.uid }}
-          path: tests_workdir/
-          overwrite: true
-          retention-days: 1
-          compression-level: 9
-          include-hidden-files: true
-
       - name: Clean up
         if: always()
         run: |

modules/nf-neuro/bundle/recognize/main.nf

@@ -23,13 +23,19 @@ process BUNDLE_RECOGNIZE {
     def rbx_processes = task.cpus ? "--processes " + task.cpus : "--processes 1"
     def outlier_alpha = task.ext.outlier_alpha ? "--alpha " + task.ext.outlier_alpha : ""
     """
+    if [[ "$transform" == *.txt ]]; then
+        ConvertTransformFile 3 $transform transform.mat --convertToAffineType \
+            && transform="transform.mat" \
+            || echo "TXT transform file conversion failed, using original file."
+    fi
+
     mkdir recobundles/
     scil_tractogram_segment_with_bundleseg ${tractograms} ${config} ${directory}/ ${transform} --inverse --out_dir recobundles/ \
         -v DEBUG $minimal_vote_ratio $seed $rbx_processes
 
     for bundle_file in recobundles/*.trk; do
-        bname=\$(basename \${bundle_file} .trk)
-        out_cleaned=${prefix}__\${bname}_cleaned.trk
+        bname=\$(basename \${bundle_file} .trk | sed 's/${prefix}_\\+//')
+        out_cleaned=${prefix}_\${bname}_cleaned.trk
         scil_bundle_reject_outliers \${bundle_file} "\${out_cleaned}" ${outlier_alpha}
     done
 
@@ -46,7 +52,7 @@ process BUNDLE_RECOGNIZE {
     scil_bundle_reject_outliers -h
 
     # dummy output for single bundle
-    touch ${prefix}__AF_L_cleaned.trk
+    touch ${prefix}_AF_L_cleaned.trk
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-neuro/bundle/recognize/tests/main.nf.test.snap

@@ -8,11 +8,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__bundle_1_cleaned.trk",
-                        "test__bundle_2_cleaned.trk",
-                        "test__bundle_3_cleaned.trk",
-                        "test__bundle_4_cleaned.trk",
-                        "test__bundle_5_cleaned.trk"
+                        "test_bundle_1_cleaned.trk",
+                        "test_bundle_2_cleaned.trk",
+                        "test_bundle_3_cleaned.trk",
+                        "test_bundle_4_cleaned.trk",
+                        "test_bundle_5_cleaned.trk"
                     ]
                 ],
                 "versions": [
@@ -21,10 +21,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-09-17T17:40:02.174844814"
+        "timestamp": "2025-10-16T16:21:06.178446125"
     },
     "bundle - recognize - stub-run": {
         "content": [
@@ -35,7 +35,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__AF_L_cleaned.trk"
+                        "test_AF_L_cleaned.trk"
                     ]
                 ],
                 "versions": [
@@ -45,9 +45,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-09-17T17:40:14.633526447"
+        "timestamp": "2025-10-16T16:21:40.42494296"
     },
     "bundle - recognize - base": {
         "content": [
@@ -58,11 +58,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__bundle_1_cleaned.trk",
-                        "test__bundle_2_cleaned.trk",
-                        "test__bundle_3_cleaned.trk",
-                        "test__bundle_4_cleaned.trk",
-                        "test__bundle_5_cleaned.trk"
+                        "test_bundle_1_cleaned.trk",
+                        "test_bundle_2_cleaned.trk",
+                        "test_bundle_3_cleaned.trk",
+                        "test_bundle_4_cleaned.trk",
+                        "test_bundle_5_cleaned.trk"
                     ]
                 ],
                 "versions": [
@@ -71,9 +71,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-09-17T17:39:29.968449034"
+        "timestamp": "2025-10-16T16:20:14.719020953"
     }
-}
+}