Merge pull request #8 from arnaudbore/add_cbrain_profile

add cbrain profile
scilus · May 3, 2021 · bd81d31 · bd81d31
2 parents 36b293b + 82ce5de
commit bd81d31
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Showing 3 changed files with 43 additions and 10 deletions.
diff --git a/USAGE b/USAGE
@@ -20,9 +20,8 @@ DESCRIPTION
     --atlas_anat                        Path to reference anatomy of the atlas
     --atlas_directory                   Path of the folder containing all atlases
 
-    NOTES
-
     OPTIONAL ARGUMENTS (current value)
+
     --atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same filename as in the atlas_config)
 
     --multi_parameters                      Number of executions for the multi-parameters ($multi_parameters)
@@ -36,7 +35,22 @@ DESCRIPTION
     --processes                             The number of parallel processes to launch ($cpu_count).
                                             Only affects the local scheduler.
 
+    --output_dir                            Directory where to write the final results.
+                                            By default, will be in "./results_rbx"
+
+
+AVAILABLE PROFILES (using -profile option (e.g. -profile large_dataset,cbrain))
+
+large_dataset                               When this profile is used, rbx_flow will be asking for 16 GB instead of 8 GB.
+
+fully_reproducible                          When this profile is used, all the parameters will be set to have 100% reproducible results.
+
+macos                                       When this profile is used, rbx_flow will modify a parameter (scratch) for MacOS users.
+
+cbrain                                      When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.
+
+NOTES
+
 Use '-C config_file.config' to specify a non-default configuration file.
 The '-C config_file.config' must be inserted after the nextflow call
 like 'nextflow -C config_file.config run ...'.
-
diff --git a/main.nf b/main.nf
@@ -13,7 +13,8 @@ if(params.help) {
                 "seeds":"$params.seeds",
                 "outlier_alpha":"$params.outlier_alpha",
                 "register_processes":"$params.register_processes",
-                "rbx_processes":"$params.rbx_processes"]
+                "rbx_processes":"$params.rbx_processes",
+                "cpu_count":"$cpu_count"]
 
     engine = new groovy.text.SimpleTemplateEngine()
     template = engine.createTemplate(usage.text).make(bindings)
@@ -107,8 +108,9 @@ process Register_Anat {
     file "${sid}__outputWarped.nii.gz"
     script:
     """
+    export ANTS_RANDOM_SEED=1234
     antsRegistrationSyNQuick.sh -d 3 -f ${native_anat} -m ${atlas} -n ${params.register_processes} -o ${sid}__output -t a
-    """ 
+    """
 }
 
 
@@ -124,7 +126,7 @@ process Transform_Centroids {
     script:
     """
     scil_apply_transform_to_tractogram.py ${centroid} ${anat} ${transfo} ${sid}__${centroid.baseName}.trk --inverse --cut_invalid
-    """ 
+    """
 }
 
 
@@ -153,7 +155,7 @@ process Recognize_Bundles {
         --tractogram_clustering_thr $params.wb_clustering_thr --seeds $params.seeds --processes $params.rbx_processes
     rm tractogram_ic.trk
     mv tmp/* ./
-    """ 
+    """
 }
 
 bundles_for_cleaning
@@ -168,7 +170,7 @@ process Clean_Bundles {
     bname = bundle.name.take(bundle.name.lastIndexOf('.'))
     """
     scil_outlier_rejection.py ${bundle} "${sid}__${bname}_cleaned.trk" --alpha $params.outlier_alpha
-    """ 
+    """
 }
 
 bundle_for_density
@@ -185,7 +187,7 @@ process Compute_Density_Bundles {
     scil_apply_transform_to_tractogram.py $bundle $atlas $transfo tmp.trk --remove_invalid
     scil_compute_streamlines_density_map.py tmp.trk "${sid}__${bname}_density.nii.gz"
     scil_image_math.py lower_threshold "${sid}__${bname}_density.nii.gz" 1 "${sid}__${bname}_binary.nii.gz"
-    """ 
+    """
 }
 
 
@@ -204,5 +206,5 @@ process Average_Bundles {
     """
     scil_image_math.py addition *_density.nii.gz 0 ${bname}_density.nii.gz
     scil_image_math.py addition *_binary.nii.gz 0 ${bname}_binary.nii.gz
-    """ 
+    """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -26,6 +26,12 @@ params {
         register_processes=4
         rbx_processes=4
         params.rbx_memory_limit='8 GB'
+
+    //**Process control**//
+        processes = false
+
+    //**Output directory**//
+        output_dir=false
 }
 
 if(params.processes) {
@@ -56,4 +62,15 @@ profiles {
     macos {
             process.scratch="/tmp"
     }
+
+    cbrain {
+      process{
+        if(params.output_dir) {
+          publishDir = [path: {"$params.output_dir/$sid/$task.process"}, mode: 'copy']
+        }
+        else{
+          publishDir = [path: {"./results_rbx/$sid/$task.process"}, mode: 'copy']
+        }
+      }
+    }
 }