Update to scilpy 1.6.0

README.md

@@ -3,6 +3,9 @@ Tractometry pipeline
 
 [![GitHub release (latest by date)](https://img.shields.io/github/v/release/scilus/tractometry_flow)](https://github.com/scilus/tractometry_flow/releases)
 
+[![Nextflow](https://img.shields.io/badge/nextflow-21.10.6-brightgreen.svg)](https://www.nextflow.io/)
+[![Docker container badge](https://img.shields.io/docker/v/scilus/scilus?label=docker&logo=docker&logoColor=white)](https://hub.docker.com/r/scilus/scilus)
+
 This pipeline allows you to extract tractometry information by combining
 subjects's fiber bundles and diffusion MRI metrics.
 
@@ -30,15 +33,14 @@ Requirements
 Singularity/Docker
 -----------
 If you are on Linux, we recommend using the Singularity to run tractometry_flow pipeline.
-If you have Singularity == 3.*, launch your Nextflow command with:
-`-with-singularity scilus/scilus:1.2.0_tractometryflow-1.0.0`
+If you have Apptainer (Singularity), launch your Nextflow command with:
+`-with-singularity ABSOLUTE_PATH/scilus-1.6.0.sif`
 
-If you have rebuild singularity Singularity == 2.* image is available [here](http://scil.dinf.usherbrooke.ca/en/containers_list/scilus-1.2.0_tractometryflow-1.0.0.img)
-Launch your Nextflow command with: `-with-singularity ABSOLUTE_PATH/scilus-1.2.0_tractometryflow-1.0.0.img`
+Image is available [here](http://scil.dinf.usherbrooke.ca/en/containers_list/scilus-1.6.0.sif)
 
 If you are on MacOS or Windows, we recommend using the Docker container to run tractometry_flow pipeline.
 Launch your Nextflow command with:
-`-with-docker scilus/scilus:1.2.0_tractometryflow-1.0.0`
+`-with-docker scilus/scilus:1.6.0`
 
 Usage
 -----

USAGE

@@ -54,7 +54,7 @@ DESCRIPTION
 
                             All subjects in the [root] folder must contain
                             pre-computed centroids if pre-computed centroids
-                            are provided. In other words, you can't mix
+                            are provided. In other words, you can not mix
                             subjects with and without pre-computed centroids
 
 
@@ -78,13 +78,22 @@ OPTIONAL ARGUMENTS (current value)
 --output_dir                                Directory where to write the final results.
                                             By default, will be in "./results_tractometry"
 
+
+AVAILABLE PROFILES (using -profile option (e.g. -profile macos, cbrain))
+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
 
-The `scilpy/scripts` folder should be in your PATH environment variable
+The 'scilpy/scripts' folder should be in your PATH environment variable. Not necessary if the
+Singularity container is used.
 
-The intermediate working directory is, by default, set to "./work".
+The intermediate working directory is, by default, set to './work'.
 To change it, use the '-w WORK_DIR' argument.
 
-Use `-C config_file.config` to specify a non-default configuration file.
-
-If running this on OSX, use `-profile osx` to get the correct shell.
+The default config file is tractoflow/nextflow.config.
+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 ...'.

main.nf

@@ -49,7 +49,7 @@ workflow.onComplete {
 Channel
     .fromFilePairs("$params.input/**/bundles/*.trk",
                    size: -1) { it.parent.parent.name }
-    .into{bundles_for_rm_invalid; in_bundles_check; bundles_for_fixel_afd}
+    .into{bundles_for_rm_invalid; in_bundles_check}
 
 Channel
     .fromFilePairs("$params.input/**/metrics/*.nii.gz",
@@ -102,6 +102,32 @@ process Rename_Metrics {
     done
     """
 }
+
+process Remove_Invalid_Streamlines {
+    input:
+    set sid, file(bundles) from bundles_for_rm_invalid
+
+    output:
+    set sid, "${sid}__*_ic.trk" into bundles_for_label_and_distance_map, bundles_for_centroids, bundles_for_fixel_afd
+
+    script:
+    String bundles_list = bundles.join(", ").replace(',', '')
+    """
+    for bundle in $bundles_list;
+      do if [[ \$bundle == *"__"* ]]; then
+          pos=\$((\$(echo \$bundle | grep -b -o __ | cut -d: -f1)+2))
+          bname=\${bundle:\$pos}
+          bname=\$(basename \$bname .trk)
+      else
+          bname=\$(basename \$bundle .trk)
+      fi
+      bname=\${bname/$params.bundle_suffix_to_remove/}
+
+      scil_remove_invalid_streamlines.py \$bundle ${sid}__\${bname}_ic.trk --remove_single_point --remove_overlapping_points --cut_invalid --no_empty
+    done
+    """
+}
+
 bundles_for_fixel_afd
     .join(fodf_for_fixel_afd)
     .set{bundle_fodf_for_fixel_afd}
@@ -132,31 +158,6 @@ process Fixel_AFD {
     """
 }
 
-process Remove_Invalid_Streamlines {
-    input:
-    set sid, file(bundles) from bundles_for_rm_invalid
-
-    output:
-    set sid, "${sid}__*_ic.trk" into bundles_for_label_and_distance_map, bundles_for_centroids optional true
-
-    script:
-    String bundles_list = bundles.join(", ").replace(',', '')
-    """
-    for bundle in $bundles_list;
-      do if [[ \$bundle == *"__"* ]]; then
-          pos=\$((\$(echo \$bundle | grep -b -o __ | cut -d: -f1)+2))
-          bname=\${bundle:\$pos}
-          bname=\$(basename \$bname .trk)
-      else
-          bname=\$(basename \$bundle .trk)
-      fi
-      bname=\${bname/$params.bundle_suffix_to_remove/}
-
-      scil_remove_invalid_streamlines.py \$bundle ${sid}__\${bname}_ic.trk --remove_single_point --remove_overlapping_points --cut_invalid --no_empty
-    done
-    """
-}
-
 process Bundle_Centroid {
     input:
     set sid, file(bundles) from bundles_for_centroids
@@ -477,7 +478,7 @@ process Bundle_Metrics_Stats_In_Endpoints {
         mv \$map \${bname}_head.nii.gz
         mv \${map/_head/_tail} \${bname}_tail.nii.gz
 
-        b_metrics=($metrics)
+        b_metrics="$metrics"
         if [[ -f \${bname}_afd_metric.nii.gz ]];
         then
             mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
@@ -531,7 +532,7 @@ process Bundle_Endpoints_Metrics {
     bname=\${bname/_uniformized/}
     mkdir \${bname}
 
-    b_metrics=($metrics)
+    b_metrics="$metrics"
     if [[ -f \${bname}_afd_metric.nii.gz ]];
     then
         mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
@@ -582,7 +583,7 @@ process Bundle_Mean_Std {
         bname=\${bname/_uniformized/}
         mv \$bundle \$bname.trk
 
-        b_metrics=($metrics)
+        b_metrics="$metrics"
         if [[ -f \${bname}_afd_metric.nii.gz ]];
         then
             mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz
@@ -720,7 +721,7 @@ process Bundle_Mean_Std_Per_Point {
         label_map=${sid}__\${bname}_labels.nii.gz
         distance_map=${sid}__\${bname}_distances.nii.gz
 
-        b_metrics=($metrics)
+        b_metrics="$metrics"
         if [[ -f \${bname}_afd_metric.nii.gz ]];
         then
             mv \${bname}_afd_metric.nii.gz afd_metric.nii.gz

nextflow.config

@@ -94,4 +94,10 @@ profiles {
     macos {
             process.scratch="/tmp"
     }
+
+    cbrain {
+      process{
+        publishDir = [path: {"./results_rbx/$sid/$task.process"}, mode: 'copy']
+      }
+    }
 }