Add participant selection flag to babs-init config yaml file

docs/source/walkthrough.rst

@@ -286,8 +286,8 @@ Below is an example YAML file for toy BIDS App:
 
 As you can see, there are several sections in this YAML file.
 
-Here, in section ``singularity_run``,
-both ``--dummy`` and ``-v`` are dummy arguments to this toy BIDS Apps:
+Here, in section ``singularity_run``, ``$SUBJECT_SELECTION_FLAG`` designates the flag used for selecting participants in the BIDS app.
+. Additionally, both ``--dummy`` and ``-v`` are dummy arguments to this toy BIDS Apps:
 argument ``--dummy`` can take any value afterwards, whereas argument ``-v`` does not take values.
 Here we use these arguments to show examples of:
 

notebooks/eg_fmriprep-20-2-3_anatonly.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-20-2-3_ingressed-fs.yaml

@@ -18,6 +18,7 @@
 #     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
 #     --input freesurfer <path/to/cloned_freesurfer_output_ria>    # 2nd input dataset \
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
     --n_cpus: '1'

notebooks/eg_fmriprep-20-2-3_regular.yaml

@@ -12,6 +12,7 @@
 
 # Arguments when executing the BIDS App using `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-23-1-3_anatonly.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: "1"
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-23-1-3_ingressed-fs.yaml

@@ -18,6 +18,7 @@
 #     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
 #     --input fmriprep_anat <path/to/cloned_fmriprep_anat_output_ria>    # 2nd input dataset \
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'

notebooks/eg_fmriprep-23-1-3_regular.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""

notebooks/eg_qsiprep-0-18-1_regular.yaml

@@ -11,6 +11,7 @@
 #   Therefore, please change and tailor it for your case before use it!!!
 
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -v: "-v"
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
     --n_cpus: "2"   # For SGE clusters: you can use "$NSLOTS" here if `number_of_cpus` is set

notebooks/eg_toybidsapp-0-0-7_rawBIDS-walkthrough.yaml

@@ -20,6 +20,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     --no-zipped: ""
     --dummy: "2"
     -v: ""

notebooks/eg_toybidsapp-0-0-7_zipped.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     --zipped: ""    # for zipped input dataset
     --dummy: "2"   # this is a dummy variable, accepting values
     -v: ""    # this is also a dummy variable, not accepting values

notebooks/eg_xcpd-0-4-0_nifti.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized BABS.
     --despike: ""
     --lower-bpf: "0.01"