downloads as inputs

hippunfold/config/snakebids.yml

@@ -471,14 +471,14 @@ nnunet_model:
   synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
   synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
 
-atlas_files_osf:
+atlas_links_osf:
   multihist7: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip='
   bigbrain: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
   magdeburg: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
   freesurfer: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
 #https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
 
-template_files_osf:
+template_links_osf:
   CITI168: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
   dHCP: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
   MBMv2: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='

hippunfold/workflow/rules/downloads.smk

@@ -25,19 +25,30 @@ rule download_model:
 
 rule download_atlas:
     params:
-        url=lambda wildcards: config["atlas_files_osf"][wildcards.atlas],
+        url=config["atlas_links_osf"][config["atlas"][0]],
     output:
-        model_zip=os.path.join(download_dir,"{atlas}"+'.zip')
+        model_zip=os.path.join(download_dir,config["atlas"][0]+'.zip')
     container:
         config["singularity"]["autotop"]
     shell:
         "wget https://{params.url} -O {output.model_zip}"
 
 rule download_template:
     params:
-        url=lambda wildcards: config["template_files_osf"][wildcards.atlas],
+        url=config["template_links_osf"][config["template"]],
     output:
-        model_zip=os.path.join(download_dir,"{template}"+'.zip')
+        model_zip=os.path.join(download_dir,config["template"]+'.zip')
+    container:
+        config["singularity"]["autotop"]
+    shell:
+        "wget https://{params.url} -O {output.model_zip}"
+
+
+rule download_template_shape:
+    params:
+        url=config["template_links_osf"][config["inject_template"]],
+    output:
+        model_zip=os.path.join(download_dir,config["inject_template"]+'.zip')
     container:
         config["singularity"]["autotop"]
     shell:
@@ -48,19 +59,34 @@ def atlas_outs():
     outs = []
     for a in config["atlas"]:
         for fn in config["atlas_files"][a]:
-            outs.append(os.path.join(download_dir,config["atlas_files"][a][fn]))
-    return outs
+            for hemi in ['L','R']:
+                outs.append(download_dir + '/' +
+                    expand(config["atlas_files"][a][fn],hemi=hemi)[0])
+    return list(dict.fromkeys(outs))
 
 def template_outs():
     outs = []
     for fn in config["template_files"][config["template"]]:
-        outs.append(os.path.join(download_dir,config["template_files"][config["template"]][fn]))
-    return outs
+        for hemi in ['L','R']:
+            for dir in ['AP','PD','IO']:
+                outs.append(download_dir + '/' +
+                    expand(config["template_files"][config["template"]][fn],hemi=hemi,dir=dir)[0])
+    return list(dict.fromkeys(outs))
+
+def template_shape_outs():
+    outs = []
+    for fn in config["template_files"][config["inject_template"]]:
+        for hemi in ['L','R']:
+            for dir in ['AP','PD','IO']:
+                for autotop in ['hipp','dentate']:
+                    outs.append(download_dir + '/' +
+                        expand(config["template_files"][config["inject_template"]][fn],hemi=hemi,dir=dir,autotop=autotop)[0])
+    return list(dict.fromkeys(outs))
 
 
 rule unzip_template:
     input:
-        model_zip=os.path.join(download_dir,"{template}"+'.zip'),
+        model_zip=os.path.join(download_dir,config["template"]+'.zip'),
     params:
         dir=download_dir,
     output:
@@ -70,7 +96,7 @@ rule unzip_template:
 
 rule unzip_atlas:
     input:
-        model_zip=os.path.join(download_dir,"{atlas}"+'.zip'),
+        model_zip=os.path.join(download_dir,config["atlas"][0]+'.zip'),
     params:
         dir=download_dir,
     output:
@@ -85,10 +111,7 @@ rule unzip_template_shape:
     params:
         dir=download_dir,
     output:
-        template_seg=os.path.join(
-            download_dir,
-            config["template_files"][config["inject_template"]]["dseg"],
-        )
+        template_shape_outs()
     shell:
         "unzip {input.model_zip} -d {params.dir}"
 

hippunfold/workflow/rules/gifti.smk

@@ -485,7 +485,7 @@ rule metric_to_nii:
     group:
         "subj"
     shell:
-        "wb_command -metric-to-volume-mapping {input.metric_gii} {input.unfoldedsurf} {params.refflatnii} {output.metric_nii} {params.interp}"
+        "wb_command -metric-to-volume-mapping {input.metric_gii} {input.unfoldedsurf} {input.refflatnii} {output.metric_nii} {params.interp}"
 
 
 rule unfolded_registration:
@@ -590,7 +590,7 @@ rule unfolded_registration:
         mem_mb=16000,
         time=10,
     shell:
-        "antsRegistrationSyNQuick.sh {params.antsparams} -f {params.refthickness} -f {params.refcurvature} -f {params.refgyrification} -m {input.thickness} -m {input.curvature} -m {input.gyrification} -o {params.outsuffix} &> {log} && "
+        "antsRegistrationSyNQuick.sh {params.antsparams} -f {input.refthickness} -f {input.refcurvature} -f {input.refgyrification} -m {input.thickness} -m {input.curvature} -m {input.gyrification} -o {params.outsuffix} &> {log} && "
         "cp {params.warpfn} {output.warp} && "
         "cp {params.invwarpfn} {output.invwarp}"
 
@@ -1114,8 +1114,7 @@ rule nii_to_label_gii:
             "tpl-avg_space-unfold_den-{density}_midthickness.surf.gii",
         ),
         label_list=lambda wildcards: os.path.join(
-            workflow.basedir,
-            "..",
+            download_dir,
             config["atlas_files"][wildcards.atlas]["label_list"],
         ),
     params:

hippunfold/workflow/rules/preproc_t1.smk

@@ -272,13 +272,11 @@ rule warp_t1_to_corobl_crop:
             type_="itk"
         ),
         ref=os.path.join(
-            workflow.basedir,
-            "..",
+            download_dir,
             config["template_files"][config["template"]]["crop_ref"],
         ),
         std_to_cor=os.path.join(
-            workflow.basedir,
-            "..",
+            download_dir,
             config["template_files"][config["template"]]["xfm_corobl"],
         ),
     output:

hippunfold/workflow/rules/qc.smk

@@ -51,12 +51,8 @@ rule get_subfield_vols_subj:
             allow_missing=True,
         ),
         lookup_tsv=os.path.join(
-            workflow.basedir,
-            "..",
-            "resources",
-            "atlases-unfolded",
-            "{atlas}",
-            "desc-subfields_atlas-{atlas}_dseg.tsv",
+            download_dir,
+            config["atlas_files"][config["atlas"][0]]["label_list"]
         ),
     group:
         "subj"