diff --git a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
index 9dff5cbe..0ad4d8f2 100644
--- a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
+++ b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
@@ -3,7 +3,7 @@
     "description": "fmriprep",
     "tool-version": "20.2.7",
     "schema-version": "0.5",
-    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] fmriprep [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [ANAT_ONLY] [BOILERPLATE_ONLY] [MD_ONLY_BOILERPLATE] [AROMA_ERR_ON_WARN] [VERBOSE_COUNT] [IGNORE] [LONGITUDINAL] [OUTPUT_SPACES] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [MEDIAL_SURFACE_NAN] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [USE_AROMA] [AROMA_MELODIC_DIM] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [CIFTI_OUTPUT] [RUN_RECONALL] [OUTPUT_LAYOUT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [REPORTS_ONLY] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG] [SLOPPY]",
+    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [ANAT_ONLY] [BOILERPLATE_ONLY] [MD_ONLY_BOILERPLATE] [AROMA_ERR_ON_WARN] [VERBOSE_COUNT] [IGNORE] [LONGITUDINAL] [OUTPUT_SPACES] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [MEDIAL_SURFACE_NAN] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [USE_AROMA] [AROMA_MELODIC_DIM] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [CIFTI_OUTPUT] [RUN_RECONALL] [OUTPUT_LAYOUT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [REPORTS_ONLY] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG] [SLOPPY]",
     "inputs": [
         {
             "id": "bids_dir",
diff --git a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
index 481e8b0e..ac915088 100644
--- a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
+++ b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
@@ -3,7 +3,7 @@
     "description": "fmriprep",
     "tool-version": "23.1.3",
     "schema-version": "0.5",
-    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] fmriprep [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [SLOPPY] [ANAT_ONLY] [BOILERPLATE_ONLY] [REPORTS_ONLY] [IGNORE] [OUTPUT_SPACES] [LONGITUDINAL] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [ME_T2S_FIT_METHOD] [OUTPUT_LAYOUT] [ME_OUTPUT_ECHOS] [MEDIAL_SURFACE_NAN] [PROJECT_GOODVOXELS] [MD_ONLY_BOILERPLATE] [CIFTI_OUTPUT] [USE_AROMA] [AROMA_MELODIC_DIM] [AROMA_ERR_ON_WARN] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [RUN_RECONALL] [TRACK_CARBON] [COUNTRY_CODE] [VERSION] [VERBOSE_COUNT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG]",
+    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [SLOPPY] [ANAT_ONLY] [BOILERPLATE_ONLY] [REPORTS_ONLY] [IGNORE] [OUTPUT_SPACES] [LONGITUDINAL] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [ME_T2S_FIT_METHOD] [OUTPUT_LAYOUT] [ME_OUTPUT_ECHOS] [MEDIAL_SURFACE_NAN] [PROJECT_GOODVOXELS] [MD_ONLY_BOILERPLATE] [CIFTI_OUTPUT] [USE_AROMA] [AROMA_MELODIC_DIM] [AROMA_ERR_ON_WARN] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [RUN_RECONALL] [TRACK_CARBON] [COUNTRY_CODE] [VERSION] [VERBOSE_COUNT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG]",
     "inputs": [
         {
             "id": "bids_dir",
diff --git a/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2.json b/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2.json
index a658878b..57e000b4 100644
--- a/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2.json
+++ b/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2.json
@@ -3,7 +3,7 @@
     "description": "heudiconv",
     "tool-version": "0.12.2",
     "schema-version": "0.5",
-    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] heudiconv [VERSION] [DICOM_DIR_TEMPLATE] [FILES] [SUBJS] [CONVERTER] [OUTDIR] [LOCATOR] [CONV_OUTDIR] [ANON_CMD] [HEURISTIC] [WITH_PROV] [SESSION] [BIDS_OPTIONS] [OVERWRITE] [DATALAD] [DEBUG] [COMMAND] [GROUPING] [MINMETA] [RANDOM_SEED] [DCMCONFIG] [QUEUE] [QUEUE_ARGS]",
+    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [VERSION] [DICOM_DIR_TEMPLATE] [FILES] [SUBJS] [CONVERTER] [OUTDIR] [LOCATOR] [CONV_OUTDIR] [ANON_CMD] [HEURISTIC] [WITH_PROV] [SESSION] [BIDS_OPTIONS] [OVERWRITE] [DATALAD] [DEBUG] [COMMAND] [GROUPING] [MINMETA] [RANDOM_SEED] [DCMCONFIG] [QUEUE] [QUEUE_ARGS]",
     "inputs": [
         {
             "name": "version",
diff --git a/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json b/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json
index 52f8c69d..764ebb66 100644
--- a/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json
+++ b/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json
@@ -3,7 +3,7 @@
     "description": "mriqc",
     "tool-version": "23.1.0",
     "schema-version": "0.5",
-    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] mriqc [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [VERBOSE_COUNT] [SPECIES] [PARTICIPANT_LABEL] [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES] [DSNAME] [BIDS_DATABASE_DIR] [BIDS_DATABASE_WIPE] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [DEBUG] [FLOAT32] [PDB] [WORK_DIR] [VERBOSE_REPORTS] [REPORTS_ONLY] [WRITE_GRAPH] [DRY_RUN] [RESOURCE_MONITOR] [USE_PLUGIN] [NO_SUB] [EMAIL] [WEBAPI_URL] [WEBAPI_PORT] [UPLOAD_STRICT] [NOTRACK] [ANTS_FLOAT] [ANTS_SETTINGS] [FFT_SPIKES_DETECTOR] [FD_THRES] [DEOBLIQUE] [DESPIKE] [START_IDX] [STOP_IDX]",
+    "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [VERBOSE_COUNT] [SPECIES] [PARTICIPANT_LABEL] [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES] [DSNAME] [BIDS_DATABASE_DIR] [BIDS_DATABASE_WIPE] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [DEBUG] [FLOAT32] [PDB] [WORK_DIR] [VERBOSE_REPORTS] [REPORTS_ONLY] [WRITE_GRAPH] [DRY_RUN] [RESOURCE_MONITOR] [USE_PLUGIN] [NO_SUB] [EMAIL] [WEBAPI_URL] [WEBAPI_PORT] [UPLOAD_STRICT] [NOTRACK] [ANTS_FLOAT] [ANTS_SETTINGS] [FFT_SPIKES_DETECTOR] [FD_THRES] [DEOBLIQUE] [DESPIKE] [START_IDX] [STOP_IDX]",
     "inputs": [
         {
             "id": "bids_dir",