From bf5b894001f913ca9f260de72ec8d255d584fe93 Mon Sep 17 00:00:00 2001
From: Mohamed Yousif <myousif9@uwo.ca>
Date: Fri, 4 Nov 2022 03:05:18 -0400
Subject: [PATCH] changing groups for mriqc & input T2 to fmriprep

---
 .gitignore                                                | 2 ++
 .vscode/settings.json                                     | 3 +++
 anat_preproc/workflow/rules/fmriprep_ciftify.smk          | 3 ++-
 .../workflow/rules/gradcorrect_mprageise_mriqc.smk        | 2 +-
 anat_preproc/workflow/rules/mprageise_mriqc.smk           | 8 ++++----
 anat_preproc/workflow/rules/mriqc_synthstrip_t1w.smk      | 2 +-
 6 files changed, 13 insertions(+), 7 deletions(-)
 create mode 100644 .vscode/settings.json

diff --git a/.gitignore b/.gitignore
index cbdd09f..3b08a44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
 **/jobs
 **/__pycache__
+**/*venv*
+**/test.txt
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..3b66410
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "git.ignoreLimitWarning": true
+}
\ No newline at end of file
diff --git a/anat_preproc/workflow/rules/fmriprep_ciftify.smk b/anat_preproc/workflow/rules/fmriprep_ciftify.smk
index 0774e7f..bda5adc 100644
--- a/anat_preproc/workflow/rules/fmriprep_ciftify.smk
+++ b/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"],
diff --git a/anat_preproc/workflow/rules/gradcorrect_mprageise_mriqc.smk b/anat_preproc/workflow/rules/gradcorrect_mprageise_mriqc.smk
index e749015..9f63ef1 100644
--- a/anat_preproc/workflow/rules/gradcorrect_mprageise_mriqc.smk
+++ b/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"
diff --git a/anat_preproc/workflow/rules/mprageise_mriqc.smk b/anat_preproc/workflow/rules/mprageise_mriqc.smk
index 98982af..1463fe2 100644
--- a/anat_preproc/workflow/rules/mprageise_mriqc.smk
+++ b/anat_preproc/workflow/rules/mprageise_mriqc.smk
@@ -8,7 +8,7 @@ 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"
@@ -16,13 +16,13 @@ rule 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:
diff --git a/anat_preproc/workflow/rules/mriqc_synthstrip_t1w.smk b/anat_preproc/workflow/rules/mriqc_synthstrip_t1w.smk
index 99524a8..c96a948 100644
--- a/anat_preproc/workflow/rules/mriqc_synthstrip_t1w.smk
+++ b/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"