Merge pull request #2 from myousif9/dev

changing groups and resources for mriqc & input T2 from synthstrip_t2w rule to fmriprep

.gitignore

@@ -1,2 +1,4 @@
 **/jobs
 **/__pycache__
+**/*venv*
+**/test.txt

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "git.ignoreLimitWarning": true
+}

anat_preproc/workflow/rules/fmriprep_ciftify.smk

@@ -80,7 +80,8 @@ rule reskstripT1w:
 
 rule fmriprep:
     input:
-        skstrip_done=rules.reskstripT1w.output.done,
+        skstrip_T1w_done = rules.reskstripT1w.output.done,
+        skstrip_T2w_done = rules.reskstripT2w.output.done if config['use_t2'] else [],
         fs_license=os.environ["FS_LICENSE"]
         if config["fs_license"] == False
         else config["fs_license"],

anat_preproc/workflow/rules/gradcorrect_mprageise_mriqc.smk

@@ -38,7 +38,7 @@ rule mriqc:
             bids(root="work", suffix="mriqc.done", **inputs.input_wildcards["uni"])
         ),
     group:
-        "subj"
+        "mriqc1"
     container:
         config["singularity"]["graham"]["mriqc"] if config["graham"] else config[
             "singularity"

anat_preproc/workflow/rules/mprageise_mriqc.smk

@@ -8,21 +8,21 @@ rule mriqc:
             bids(root="work", suffix="mriqc.done", **inputs.input_wildcards["uni"])
         ),
     group:
-        "subj"
+        "mriqc1"
     container:
         config["singularity"]["graham"]["mriqc"] if config["graham"] else config[
             "singularity"
         ]["docker"]["mriqc"]
     threads: 8
     resources:
         mem_mb=16000,
-        time=1440,
+        time=180,
     log:
         bids(root="logs", suffix="mriqc.log", **inputs.input_wildcards["uni"]),
     shell:
         """
         mriqc {input.bids_dir} {params.mriqc_dir} participant --participant-label {wildcards.subject} &> {log}
-        mriqc {params.bids_dir} {params.mriqc_dir} group
+        mriqc {input.bids_dir} {params.mriqc_dir} group
         """
 
 
@@ -51,7 +51,7 @@ rule mprageise:
     threads: 8
     resources:
         mem_mb=16000,
-        time=1440,
+        time=180,
     log:
         bids(root="logs", suffix="3dmprageise.log", **inputs.input_wildcards["uni"]),
     shell:

anat_preproc/workflow/rules/mriqc_synthstrip_t1w.smk

@@ -9,7 +9,7 @@ rule mriqc2:
             bids(root="work", suffix="mriqc2.done", **inputs.input_wildcards["uni"])
         ),
     group:
-        "subj"
+        "mriqc2"
     container:
         config["singularity"]["graham"]["mriqc"] if config["graham"] else config[
             "singularity"