Merge pull request #9 from arnaudbore/fix_rbx_processes

Fix processes and cpu count + add original anat for qc
scilus · May 3, 2021 · 9729306 · 9729306
2 parents bd81d31 + 047e9d3
commit 9729306
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diff --git a/main.nf b/main.nf
@@ -106,10 +106,12 @@ process Register_Anat {
     set sid, "${sid}__output0GenericAffine.mat" into transformation_for_recognition, transformation_for_centroids
     set sid, "${sid}__output0GenericAffine.mat" into transformation_for_average
     file "${sid}__outputWarped.nii.gz"
+    file "${sid}__native_anat.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
+    cp ${native_anat} ${sid}__native_anat.nii.gz
     """
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -25,7 +25,7 @@ params {
     //**Number of processes per tasks**//
         register_processes=4
         rbx_processes=4
-        params.rbx_memory_limit='8 GB'
+        rbx_memory_limit='8 GB'
 
     //**Process control**//
         processes = false