added initial tractoflow config

pipelines/processing/tractoflow-2.4.2/config.json

@@ -0,0 +1,20 @@
+{
+    "NAME": "tractoflow",
+    "VERSION": "2.4.2",
+    "CONTAINER_INFO": {
+        "FILE": "[[NIPOPPY_DPATH_CONTAINERS]]/[[PIPELINE_NAME]]_[[PIPELINE_VERSION]].sif",
+        "URI": "docker://bcmcpher/dmri-tractoflow:[[PIPELINE_VERSION]]"
+    },
+    "CONTAINER_CONFIG": {},
+    "STEPS": [
+        {
+            "INVOCATION_FILE": "invocation.json",
+            "DESCRIPTOR_FILE": "descriptor.json",
+            "HPC_CONFIG_FILE": "hpc.json",
+            "TRACKER_CONFIG_FILE": "tracker.json"
+        }
+    ],
+    "VARIABLES": {},
+    "PIPELINE_TYPE": "processing",
+    "SCHEMA_VERSION": "1"
+}

pipelines/processing/tractoflow-2.4.2/descriptor.json

@@ -0,0 +1,69 @@
+{
+    "name": "tractoflow",
+    "description": "Run tractoflow pipeline with some semblance of useful file handling.",
+    "tool-version": "2.4.2",
+    "schema-version": "0.5",
+    "command-line": "bash /opt/tf-wrapper/run_tractoflow.sh [PARTICIPANT_LABEL] [SESSION_LABEL] [BIDS_DIR] [WORK_DIR] [OUTPUT_DIR] [TF_INPUT_DIR]",
+    "container-image": {
+        "type": "docker",
+        "image": "bcmcpher/dmri-tractoflow:1.0.0",
+        "tag": "latest",
+        "uri": "docker://bcmcpher/dmri-tractoflow:1.0.0"
+    },
+    "inputs": [
+        {
+            "id": "subject",
+            "name": "subject",
+            "description": "The subject ID to be processed.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[PARTICIPANT_LABEL]"
+        },
+        {
+            "id": "session",
+            "name": "session",
+            "description": "The session ID to be processed.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[SESSION_LABEL]"
+        },
+        {
+            "id": "bids_dir",
+            "name": "bids_dir",
+            "description": "The preprocessed DWI .nii.gz file used to fit the DTI / fwDTI model.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[BIDS_DIR]"
+        },
+        {
+            "id": "work_dir",
+            "name": "work_dir",
+            "description": "The derivatives directory to write results into.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[WORK_DIR]"
+        },
+        {
+            "id": "output_dir",
+            "name": "output_dir",
+            "description": "The directory to write results.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[OUTPUT_DIR]"
+        },
+        {
+            "id": "tf_input_dir",
+            "name": "tf_input_dir",
+            "description": "The directory where cleaned / merged dMRI files are created.",
+            "optional": false,
+            "type": "String",
+            "value-key": "[TF_INPUT_DIR]"
+        }
+    ],
+    "tags": {},
+    "suggested-resources": {
+        "cpu-cores": 4,
+        "ram": 16,
+        "walltime-estimate": 120
+    }
+}

pipelines/processing/tractoflow-2.4.2/hpc.json

@@ -0,0 +1,7 @@
+{
+    "ACCOUNT": "[[HPC_ACCOUNT_NAME]]",
+    "TIME": "8:00:00",
+    "CORES": "8",
+    "MEMORY": "32G",
+    "ARRAY_CONCURRENCY_LIMIT": "25"
+}

pipelines/processing/tractoflow-2.4.2/invocation.json

@@ -0,0 +1,8 @@
+{
+    "subject": "[[NIPOPPY_PARTICIPANT_ID]]",
+    "session": "[[NIPOPPY_SESSION_ID]]",
+    "bids_dir": "[[NIPOPPY_DPATH_BIDS]]",
+    "work_dir": "[[NIPOPPY_DPATH_PIPELINE_WORK]]",
+    "output_dir": "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]",
+    "tf_input_dir": "[[NIPOPPY_DPATH_PIPELINE]]/input"
+}

pipelines/processing/tractoflow-2.4.2/tracker.json

@@ -0,0 +1,12 @@
+{
+    "PATHS": [
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_DTI_Shell/[[NIPOPPY_PARTICIPANT_ID]]__dwi_dti.nii.gz",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_DTI_Shell/[[NIPOPPY_PARTICIPANT_ID]]__bval_dti",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_DTI_Shell/[[NIPOPPY_PARTICIPANT_ID]]__bvec_dti",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/DTI_Metrics/[[NIPOPPY_PARTICIPANT_ID]]__fa.nii.gz",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/DTI_Metrics/[[NIPOPPY_PARTICIPANT_ID]]__tensor.nii.gz",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_FODF_Shell/[[NIPOPPY_PARTICIPANT_ID]]__dwi_fodf.nii.gz",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_FODF_Shell/[[NIPOPPY_PARTICIPANT_ID]]__bval_fodf",
+        "[[NIPOPPY_BIDS_SESSION_ID]]/[[NIPOPPY_BIDS_PARTICIPANT_ID]]/Extract_FODF_Shell/[[NIPOPPY_PARTICIPANT_ID]]__bvec_fodf"
+    ]
+}

tests/conftest.py

@@ -38,6 +38,7 @@
         ("mriqc", "23.1.0", "default"),
         ("qsiprep", "0.23.0", "default"),
         ("qsiprep", "1.0.1", "default"),
+        ("tractoflow", "2.4.2", "default"),
     ),
     PipelineTypeEnum.EXTRACTION: (
         ("fs_stats", "0.2.1", "default"),